Table Of Contents Page, PNAS Volume 115, Number 8
This Week in PNAS
Letters (Online Only)
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Nutritional and greenhouse gas impacts of removing animals from US agriculture
View related content:Feedlot diet for Americans that results from a misspecified optimization algorithm
Without animals, US farmers would reduce feed crop production
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Causing confusion in the debate about the transition toward a more plant-based diet
Nutritional and greenhouse gas impacts of removing animals from US agriculture
View related content:Feedlot diet for Americans that results from a misspecified optimization algorithm
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This article replies to:
Causing confusion in the debate about the transition toward a more plant-based diet
Feedlot diet for Americans that results from a misspecified optimization algorithm
Nutritional and greenhouse gas impacts of removing animals from US agriculture
Without animals, US farmers would reduce feed crop production
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Science and Culture
QnAs
Profiles
Commentaries
PNAS Plus Significance Statements
Physical Sciences
Applied Physical Sciences
Although the motility of the flagellated bacteria, Escherichia coli, has been widely studied, the effect of viscosity on swimming speed remains controversial.
The swimming mode of wild-type E. coli is often idealized as a run-and-tumble sequence in which ...
The diamond anvil cell (DAC) is considered one of the dominant devices to generate
ultrahigh static pressure. The development of the DAC technique has enabled researchers
to explore rich high-pressure science in the multimegabar pressure range. Here, we
...
Biophysics and Computational Biology
Studies over the past decade have highlighted the functional significance of intrinsically
disordered proteins (IDPs). Due to conformational heterogeneity and inherent dynamics,
structural studies of IDPs have relied mostly on NMR spectroscopy, despite ...
Chemistry
Marine sponges are prolific sources of unique bioactive natural products. The sponge
Theonella swinhoei is represented by several distinct variants with largely nonoverlapping chemistry.
For the Japanese chemotype Y harboring diverse complex polyketides ...
Computer simulation plays a central role in modern-day materials science. The utility
of a given computational approach depends largely on the balance it provides between
accuracy and computational cost. Molecular crystals are a class of materials of ...
This paper describes the mechanistic insight-guided development of a catalyst system,
employing a phenolic proton donor catalyst in addition to a cinchonium-derived phase-transfer
catalyst, to control the chemoselectivity of two distinct intermediates, ...
Earth, Atmospheric, and Planetary Sciences
Understanding the causes of human-induced earthquakes is paramount to reducing societal
risk. We investigated five cases of seismicity associated with hydraulic fracturing
(HF) in Ohio since 2013 that, because of their isolation from other injection ...
In the world-famous sediments of the Chinese Loess Plateau, fossil soils alternate
with windblown dust layers to record monsoonal variations over the last ∼3 My. The
less-weathered, weakly magnetic dust layers reflect drier, colder glaciations. The
fossil ...
Knowledge of the structure and properties of silicate magma under extreme pressure
plays an important role in understanding the nature and evolution of Earth’s deep
interior. Here we report the structure of MgSiO3 glass, considered an analog of silicate ...
Engineering
Gel layers bound to a rigid substrate are used in cell culture to control differentiation
and migration and to lower the friction and tailor the wetting of solids. Their thickness,
often considered a negligible parameter, affects cell mechanosensing or ...
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Soft wetting: Models based on energy dissipation or on force balance are equivalent
This article has a reply:Reply to Karpitschka et al.: The Neumann force balance does not hold in dynamical elastowetting
Environmental Sciences
The 2014–2015 Legionnaires’ disease (LD) outbreak in Genesee County, MI, and the outbreak
resolution in 2016 coincided with changes in the source of drinking water to Flint’s
municipal water system. Following the switch in water supply from Detroit to ...
This article has a correction:
Correction for Zahran et al., Assessment of the Legionnaires’ disease outbreak in Flint, Michigan
Ocean acidification (OA) is considered an important threat to coral reef ecosystems,
because it reduces the availability of carbonate ions that reef-building corals need
to produce their skeletons. However, while theory predicts that coral calcification
...
Physics
We use the language of uninformative Bayesian prior choice to study the selection
of appropriately simple effective models. We advocate for the prior which maximizes
the mutual information between parameters and predictions, learning as much as possible
...
Spatial patterning of periodic dynamics is a dramatic and ubiquitous ecological phenomenon
arising in systems ranging from diseases to plants to mammals. The degree to which
spatial correlations in cyclic dynamics are the result of endogenous factors ...
Statistics
The Bayesian method is noted to produce spuriously high posterior probabilities for
phylogenetic trees in analysis of large datasets, but the precise reasons for this
overconfidence are unknown. In general, the performance of Bayesian selection of ...
Genomics has revolutionized biology, enabling the interrogation of whole transcriptomes,
genome-wide binding sites for proteins, and many other molecular processes. However,
individual genomic assays measure elements that interact in vivo as components of
...
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Social Sciences
Economic Sciences
We examine how reciprocity changes over time by studying a large quasiexperiment in
the field. Specifically, we analyze administrative data from a university hospital
system. The data include information about over 18,000 donation requests made by the
...
Psychological and Cognitive Sciences
We use big data methods to investigate how decision-making might depend on future
sightedness (that is, on how far into the future people’s thoughts about the future
extend). In study 1, we establish a link between future thinking and decision-making
at ...
Personal bests act as reference points. Examining 133 million chess games, we find
that players exert effort to set new personal best ratings and quit once they have
done so. Although specific and difficult goals have been shown to inspire greater
...
The ability to detect biological motion (BM) and decipher the meaning therein is essential
to human survival and social interaction. However, at the individual level, we are
not equally equipped with this ability. In particular, impaired BM perception and
...
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Biological Sciences
Agricultural Sciences
A major unresolved issue is how the uterus influences infertility and subfertility
in cattle. Serial embryo transfer was previously used to classify heifers as high-fertile
(HF), subfertile (SF), or infertile (IF). To assess pregnancy loss, two in vivo-...
Biochemistry
Studies over the past decade have highlighted the functional significance of intrinsically
disordered proteins (IDPs). Due to conformational heterogeneity and inherent dynamics,
structural studies of IDPs have relied mostly on NMR spectroscopy, despite ...
Maintenance of genome integrity is critical for both faithful propagation of genetic
information and prevention of mutagenesis induced by various DNA damage events. Here
we report cold-inducible RNA-binding protein (CIRBP) as a newly identified key ...
Solute carrier family 39, member 14 (SLC39A14) is a transmembrane transporter that
can mediate the cellular uptake of zinc, iron, and manganese (Mn). Studies of Slc39a14 knockout (Slc39a14−/−) mice have documented that SLC39A14 is required for systemic ...
The mitotic checkpoint system ensures the fidelity of chromosome segregation in mitosis
by preventing premature initiation of anaphase until correct bipolar attachment of
chromosomes to the mitotic spindle is reached. It promotes the assembly of a mitotic
...
Tumor necrosis factor (TNF) receptor-associated factor 6 (TRAF6) plays a vital role
in immune signal transduction pathways by acting as a ubiquitin ligase (E3) for Lys63-linked
polyubiquitin chain synthesis. However, the detailed mechanism by which the ...
Although the addition of the prosthetic group lipoate is essential to the activity
of critical mitochondrial catabolic enzymes, its regulation is unknown. Here, we show
that lipoylation of the pyruvate dehydrogenase and α-ketoglutarate dehydrogenase (αKDH)...
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Histidine biosynthesis is an essential process in plants and microorganisms, making
it an attractive target for the development of herbicides and antibacterial agents.
Imidazoleglycerol-phosphate dehydratase (IGPD), a key enzyme within this pathway,
has ...
Biophysics and Computational Biology
Numerous posttranslational modifications have been described in kinesins, but their
consequences on motor mechanics are largely unknown. We investigated one of these—acetylation
of lysine 146 in Eg5—by creating an acetylation mimetic lysine to glutamine ...
Single-channel recordings are widely used to explore functional properties of ion
channels. Typically, such recordings are performed at bandwidths of less than 10 kHz
because of signal-to-noise considerations, limiting the temporal resolution available
...
α-Helical membrane proteins have eluded investigation of their thermodynamic stability
in lipid bilayers. Reversible denaturation curves have enabled some headway in determining
unfolding free energies. However, these parameters have been limited to ...
Although the motility of the flagellated bacteria, Escherichia coli, has been widely studied, the effect of viscosity on swimming speed remains controversial.
The swimming mode of wild-type E. coli is often idealized as a run-and-tumble sequence in which ...
Cell Biology
In almost all eukaryotes, mitochondria maintain their own genome. Despite the discovery
more than 50 y ago, still very little is known about how the genome is correctly segregated
during cell division. The protozoan parasite Trypanosoma brucei contains a ...
Cellular senescence is an important anticancer mechanism that restricts proliferation
of damaged or premalignant cells. Cellular senescence also plays an important role
in tissue remodeling during development. However, there is a trade-off associated
with ...
Developmental Biology
The HMG-box protein Capicua (Cic) is a conserved transcriptional repressor that functions
downstream of receptor tyrosine kinase (RTK) signaling pathways in a relatively simple
switch: In the absence of signaling, Cic represses RTK-responsive genes by ...
Robust morphogenetic events are pivotal for animal embryogenesis. However, comparison
of the modes of development of different members of a phylum suggests that the spectrum
of developmental trajectories accessible for a species might be far broader than ...
The distinction of anterior versus posterior is a crucial first step in animal embryogenesis.
In the fly Drosophila, this axis is established by morphogenetic gradients contributed by the mother that
regulate zygotic target genes. This principle has been ...
Ecology
Ocean acidification (OA) is considered an important threat to coral reef ecosystems,
because it reduces the availability of carbonate ions that reef-building corals need
to produce their skeletons. However, while theory predicts that coral calcification
...
Spatial patterning of periodic dynamics is a dramatic and ubiquitous ecological phenomenon
arising in systems ranging from diseases to plants to mammals. The degree to which
spatial correlations in cyclic dynamics are the result of endogenous factors ...
Managing natural resources in an era of increasing climate impacts requires accounting
for the synergistic effects of climate, ecosystem changes, and harvesting on resource
productivity. Coincident with recent exceptional warming of the northwest Atlantic
...
View related content:
Knowledge about the biogeographic affinities of the world’s tropical forests helps
to better understand regional differences in forest structure, diversity, composition,
and dynamics. Such understanding will enable anticipation of region-specific ...
This article has a correction:
Correction for Slik et al., Phylogenetic classification of the world’s tropical forests
The Earth’s ecosystems are under unprecedented pressure, yet the nature of contemporary
biodiversity change is not well understood. Growing evidence that community size is
regulated highlights the need for improved understanding of community dynamics. As
...
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Many studies report that mountain plant species are shifting upward in elevation.
However, the majority of these reports focus on shifts of upper limits. Here, we expand
the focus and simultaneously analyze changes of both range limits, optima, and ...
Environmental Sciences
The 2014–2015 Legionnaires’ disease (LD) outbreak in Genesee County, MI, and the outbreak
resolution in 2016 coincided with changes in the source of drinking water to Flint’s
municipal water system. Following the switch in water supply from Detroit to ...
This article has a correction:
Correction for Zahran et al., Assessment of the Legionnaires’ disease outbreak in Flint, Michigan
Evolution
Symbiotic associations play a pivotal role in multicellular life by facilitating acquisition
of new traits and expanding the ecological capabilities of organisms. In insects that
are obligatorily dependent on intracellular bacterial symbionts, novel host ...
The Bayesian method is noted to produce spuriously high posterior probabilities for
phylogenetic trees in analysis of large datasets, but the precise reasons for this
overconfidence are unknown. In general, the performance of Bayesian selection of ...
How can altruism evolve or be maintained in a selfish world? Hamilton’s rule shows
that the former process will occur when rb > c—the benefits to the recipients of an altruistic act b, weighted by the relatedness between the social partners r, exceed the ...
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Cooperative breeding and the evolutionary coexistence of helper and nonhelper strategies
View related content:No evidence for a heritable altruism polymorphism in Tibetan ground tits
This article has a reply:Reply to Gilbert: On the relationship between association and altruism
When different species experience similar selection pressures, the probability of
evolving similar adaptive solutions may be influenced by legacies of evolutionary
history, such as lineage-specific changes in genetic background. Here we test for
adaptive ...
Genetics
Eukaryotes respond to amino acid starvation by enhancing the translation of mRNAs
encoding b-ZIP family transcription factors (GCN4 in Saccharomyces cerevisiae and ATF4 in mammals), which launch transcriptional programs to counter this stress. This ...
Polycomb group (PcG) proteins maintain the silenced state of key developmental genes
in animals, but how these proteins are recruited to specific regions of the genome
is still poorly understood. In Drosophila, PcG proteins are recruited to Polycomb ...
Genitourinary (GU) birth defects are among the most common yet least studied congenital
malformations. Congenital anomalies of the kidney and urinary tract (CAKUTs) have
high morbidity and mortality rates and account for ∼30% of structural birth defects.
...
In individuals with autism spectrum disorder (ASD), de novo mutations have previously
been shown to be significantly correlated with lower IQ but not with the core characteristics
of ASD: deficits in social communication and interaction and restricted ...
Aneuploidy is a feature of most cancer cells, and a myriad of approaches have been
developed to detect it in clinical samples. We previously described primers that could
be used to amplify ∼38,000 unique long interspersed nucleotide elements (LINEs) from
...
Immunology and Inflammation
HIV controllers (HCs) are individuals who can naturally control HIV infection, partially
due to potent HIV-specific CD8+ T cell responses. Here, we examined the hypothesis
that superior function of CD8+ T cells from HCs is encoded by their T cell ...
For many cancer types, incidence rises rapidly with age as an apparent power law,
supporting the idea that cancer is caused by a gradual accumulation of genetic mutations.
Similarly, the incidence of many infectious diseases strongly increases with age.
...
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Are most cancer cases a consequence of an immune deficiency caused by thymic involution?
Strengthening the immune system for cancer prevention
Shortcomings of the immunological model of carcinogenesis
This article has a reply:Unlike αβ-T lineage cells, where the role of ligand in intrathymic selection is well
established, the role of ligand in the development of γδ-T cells remains controversial.
Here we provide evidence for the role of a bona fide selecting ligand in shaping ...
View related content:
Does selecting ligand shape γδ-TCR repertoire?
This article has a reply:Reply to Chien: Clarification of the effect of ligand on γδ-TCR repertoire selection
Impaired wound closure is a growing medical problem associated with metabolic diseases
and aging. Immune cells play important roles in wound healing by following instructions
from the microenvironment. Here, we developed a technology to bioengineer the ...
A hallmark of B-cell immunity is the generation of a diverse repertoire of antibodies
from a limited set of germline V(D)J genes. This repertoire is usually defined in
terms of amino acid composition. However, variable domains may also acquire N-linked ...
Medical Sciences
Moxetumomab pasudotox (Moxe) is a chimeric protein composed of an anti-CD22 Fv fused
to a portion of Pseudomonas exotoxin A and kills CD22-expressing leukemia cells. It is very active in hairy-cell
leukemia, but many children with relapsed/refractory ...
Cysteinyl-leukotrienes (cys-LTs) are 5-lipoxygenase-derived lipid mediators involved
in the pathogenesis and progression of inflammatory disorders, in particular asthma.
We have previously found evidence linking these mediators to increased levels of ...
Polo-like kinase 4 (PLK4) is a serine/threonine kinase regulating centriole duplication.
CFI-400945 is a highly selective PLK4 inhibitor that deregulates centriole duplication,
causing mitotic defects and death of aneuploid cancers. Prior work was ...
View related content:
CFI-400945 is not a selective cellular PLK4 inhibitor
This article has a reply:Reply to Oegema et al.: CFI-400945 and Polo-like kinase 4 inhibition
Microbiology
Marine sponges are prolific sources of unique bioactive natural products. The sponge
Theonella swinhoei is represented by several distinct variants with largely nonoverlapping chemistry.
For the Japanese chemotype Y harboring diverse complex polyketides ...
Neuroscience
Emerging findings suggest that compromised cellular bioenergetics and DNA repair contribute
to the pathogenesis of Alzheimer’s disease (AD), but their role in disease-defining
pathology is unclear. We developed a DNA repair-deficient 3xTgAD/Polβ+/− mouse ...
Neuromodulation of neural networks, whereby a selected circuit is regulated by a particular
modulator, plays a critical role in learning and memory. Among neuromodulators, acetylcholine
(ACh) plays a critical role in hippocampus-dependent memory and has ...
The decline of cognitive function occurs with aging, but the mechanisms responsible
are unknown. Astrocytes instruct the formation, maturation, and elimination of synapses,
and impairment of these functions has been implicated in many diseases. These ...
Alzheimer’s disease (AD) is a leading cause of mortality among the elderly. We performed
a whole-genome sequencing study of AD in the Chinese population. In addition to the
variants identified in or around the APOE locus (sentinel variant rs73052335, P = ...
View related content:
We recently discovered 27 recurrent DNA double-strand break (DSB) clusters (RDCs)
in mouse neural stem/progenitor cells (NSPCs). Most RDCs occurred across long, late-replicating
RDC genes and were found only after mild inhibition of DNA replication. RDC ...
Physiology
Actin polymerization and assembly into stress fibers (SFs) is central to many cellular
processes. However, how SFs form in response to the mechanical interaction of cells
with their environment is not fully understood. Here we have identified Piezo2 ...
Plant Biology
Plants largely rely on plasma membrane (PM)-resident receptor-like kinases (RLKs)
to sense extracellular and intracellular stimuli and coordinate cell differentiation,
growth, and immunity. Several RLKs have been shown to undergo internalization through
...
If the highly efficient C4 photosynthesis pathway could be transferred to crops with the C3 pathway there could be yield gains of up to 50%. It has been proposed that the multiple
metabolic and developmental modifications associated with C4 photosynthesis ...
Psychological and Cognitive Sciences
The ability to detect biological motion (BM) and decipher the meaning therein is essential
to human survival and social interaction. However, at the individual level, we are
not equally equipped with this ability. In particular, impaired BM perception and
...
View related content:
Sustainability Science
Managing natural resources in an era of increasing climate impacts requires accounting
for the synergistic effects of climate, ecosystem changes, and harvesting on resource
productivity. Coincident with recent exceptional warming of the northwest Atlantic
...
View related content:
Systems Biology
The mammalian circadian clock coordinates physiology with environmental cycles through
the regulation of daily oscillations of gene expression. Thousands of transcripts
exhibit rhythmic accumulations across mouse tissues, as determined by the balance
of ...
Cells in tissues communicate by secreted growth factors (GF) and other signals. An
important function of cell circuits is tissue homeostasis: maintaining proper balance
between the amounts of different cell types. Homeostasis requires negative feedback
on ...
Genomics has revolutionized biology, enabling the interrogation of whole transcriptomes,
genome-wide binding sites for proteins, and many other molecular processes. However,
individual genomic assays measure elements that interact in vivo as components of
...
View related content:
Correction (Online Only)
Cover image: Pictured is the Alpine plant Androsace alpina. Sabine B. Rumpf et al. found that the elevational ranges of 183 plant species in the European Alps have shifted upslope compared with those reported from surveys conducted prior to 1970, and that the speed of this shift decreased with increasing elevation. The results suggest that species at the highest elevations are at risk from climate change and competitors. See the article by Sabine B. Rumpf et al. on pages 1848–1853. Image courtesy of Christian Kuehs (photographer).
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