Table Of Contents Page, PNAS Volume 106, Number 50
This Week in PNAS
Letters (Online Only)
Commentaries
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Phase-dependent neuronal coding of objects in short-term memory
Perspective
Our understanding of the initial period of agriculture in the southwestern United
States has been transformed by recent discoveries that establish the presence of maize
there by 2100 cal. B.C. (calibrated calendrical years before the Christian era) and
...
Physical Sciences
Applied Physical Sciences
Three-dimensional (3D), multi-transistor-layer, integrated circuits represent an important
technological pursuit promising advantages in integration density, operation speed,
and power consumption compared with 2D circuits. We report fully functional, 3D ...
Single- and multiple-nanopore membranes are both highly interesting for biosensing
and separation processes, as well as their ability to mimic biological membranes.
The density of pores, their shape, and their surface chemistry are the key factors
that ...
Metallic nanoscale structures are capable of supporting surface plasmon polaritons
(SPPs), propagating collective electron oscillations with tight spatial confinement
at the metal surface. SPPs represent one of the most promising structures to beat
the ...
Chemistry
Ambipolar-transporting coaxial nanotubes with a tailored molecular graphene–fullerene heterojunction
Despite a large steric bulk of C60, a molecular graphene with a covalently linked C60 pendant [hexabenzocoronene (HBC)–C60; 1] self-assembles into a coaxial nanotube whose wall consists of a graphite-like
π-stacked HBC array, whereas the nanotube surface ...
The identification of aggregation inhibitors and the investigation of their mechanism
of action are fundamental in the quest to mitigate the pathological consequences of
amyloid formation. Here, characterization of the structural and mechanistic basis
for ...
Environmental Sciences
An Euler atmospheric transport model (Canadian Model for Environmental Transport of
Organochlorine Pesticides, CanMETOP) was applied and validated to estimate polycyclic
aromatic hydrocarbon (PAH) ambient air concentrations at ground level in China based
...
Geology
In contrast with speciation in terrestrial organisms, marine plankton frequently display
gradual morphological change without lineage division (e.g., phyletic gradualism or
gradual evolution), which has raised the possibility that a different mode of ...
Physics
Bacteria serve as the central arena for understanding how gene networks and proteins
process information and control cellular behaviors. Recently, much effort has been
devoted to the investigation of specific bacteria gene circuits as functioning modules.
...
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Statistics
Prompted by the increasing interest in networks in many fields, we present an attempt
at unifying points of view and analyses of these objects coming from the social sciences,
statistics, probability and physics communities. We apply our approach to the ...
Social Sciences
Anthropology
Jola women farmers in the Casamance region of southern Senegal use their “traditional”
knowledge and farming skills to shift crop repertoires and techniques so as to embark
on market-gardening, thus innovating in response to new needs and perceived ...
Economic Sciences
Health care is a crucial factor in US economic growth, because growing health care
costs have made US corporations less competitive than their counterparts in countries
where central governments assume most of those costs. In this paper we illustrate
a ...
Psychological and Cognitive Sciences
In prevailing approaches to human sentence comprehension, the outcome of the word
recognition process is assumed to be a categorical representation with no residual
uncertainty. Yet perception is inevitably uncertain, and a system making optimal use
of ...
This article has a correction:
People with whom one is personally acquainted tend to elicit richer and more vivid
memories than people with whom one does not have a personal connection. Recent findings
from neurons in the human medial temporal lobe (MTL) have shown that individual ...
Biological Sciences
Applied Biological Sciences
The synthesis of juvenile hormone (JH) is an attractive target for control of insect
pests and vectors of disease, but the minute size of the corpora allata (CA), the
glands that synthesize JH, has made it difficult to identify important biosynthetic
...
Biochemistry
Photoactivatable fluorescent proteins (PAFPs) are required for super-resolution imaging
of live cells. Recently, the first red PAFP, PAmCherry1, was reported, which complements
the photo-activatable GFP by providing a red super-resolution color. ...
tRNAHis guanylyltransferase (Thg1) post-transcriptionally adds a G (position −1) to the 5′-terminus
of tRNAHis. The Methanosarcina acetivorans Thg1 (MaThg1) gene contains an in-frame TAG (amber) codon. Although a UAG codon typically
directs translation ...
The catalytic mechanism of DNA polymerases involves multiple steps that precede and
follow the transfer of a nucleotide to the 3′-hydroxyl of the growing DNA chain. Here
we report a single-molecule approach to monitor the movement of E. coli DNA ...
Bacterial DNA replication requires DnaA, an AAA+ ATPase that initiates replication
at a specific chromosome region, oriC, and is regulated by species-specific regulators that directly bind DnaA. HobA is
a DnaA binding protein, recently identified as an ...
The Golgi-associated four-phosphate adaptor protein 2 (FAPP2) has been shown to possess
transfer activity for glucosylceramide both in vitro and in cells. We have previously
shown that FAPP2 is involved in apical transport from the Golgi complex in ...
Starch defines an insoluble semicrystalline form of storage polysaccharides restricted
to Archaeplastida (red and green algae, land plants, and glaucophytes) and some secondary
endosymbiosis derivatives of the latter. While green algae and land-plants ...
Tail-anchored (TA) membrane proteins are involved in a variety of important cellular
functions, including membrane fusion, protein translocation, and apoptosis. The ATPase
Get3 (Asna1, TRC40) was identified recently as the endoplasmic reticulum targeting
...
The only Y-family DNA polymerase conserved among all domains of life, DinB and its
mammalian ortholog pol κ, catalyzes proficient bypass of damaged DNA in translesion
synthesis (TLS). Y-family DNA polymerases, including DinB, have been implicated in
...
Interleukin-2 tyrosine kinase (Itk) is a Tec family tyrosine kinase that mediates
signaling processes after T cell receptor engagement. Activation of Itk requires recruitment
to the membrane via its pleckstrin homology domain, phosphorylation of Itk by ...
Biophysics and Computational Biology
Bacteria serve as the central arena for understanding how gene networks and proteins
process information and control cellular behaviors. Recently, much effort has been
devoted to the investigation of specific bacteria gene circuits as functioning modules.
...
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We present here a structural and mechanistic description of how a protein changes
its fold and function, mutation by mutation. Our approach was to create 2 proteins
that (i) are stably folded into 2 different folds, (ii) have 2 different functions, and (...
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Acidianus filamentous virus 1 (AFV1), a member of the Lipothrixviridae family, infects the hyperthermophilic, acidophilic crenarchaeaon Acidianus hospitalis. The virion, covered with a lipidic outer shell, is 9,100-Å long and contains a 20.8-kb
linear ...
Cell Biology
High-energy inositol pyrophosphates, such as IP7 (diphosphoinositol pentakisphosphate), can directly donate a β-phosphate to a prephosphorylated
serine residue generating pyrophosphorylated proteins. Here, we show that the β subunit
of AP-3, a clathrin-...
The immune receptor signaling pathway is used by nonimmune cells, but the molecular
adaptations that underlie its functional diversification are not known. Circulating
platelets use the immune receptor homologue glycoprotein VI (GPVI) to respond to ...
Dynamic instability, in which abrupt transitions occur between growing and shrinking
states, is an intrinsic property of microtubules that is regulated by both mechanics
and specialized proteins. We discuss a model of dynamic instability based on the ...
Developmental Biology
Cell identity is acquired in different brain structures according to a stereotyped
timing schedule, by accommodating the proliferation of multipotent progenitor cells
and the generation of distinct types of mature nerve cells at precise times. However,
...
The adrenal cortex is a critical steroidogenic endocrine tissue, generated at least
in part from the coelomic epithelium of the urogenital ridge. Neither the intercellular
signals that regulate cortical development and maintenance nor the lineage ...
The Cul3-based E3 ubiquitin ligases regulate many cellular processes using a large
family of BTB domain–containing proteins as their target recognition components, but
how they recognize targets remains unknown. Here we identify and characterize degrons
...
Ecology
Terrestrial organic matter inputs have long been thought to play an important role
in aquatic food web dynamics. Results from recent whole lake 13C addition experiments suggest terrestrial particulate organic carbon (t-POC) inputs
account for a ...
Plants under herbivore attack are able to initiate indirect defense by synthesizing
and releasing complex blends of volatiles that attract natural enemies of the herbivore.
However, little is known about how plants respond to infestation by multiple ...
Natural bacterial communities are extremely diverse and highly dynamic, but evidence
is mounting that the compositions of these communities follow predictable temporal
patterns. We investigated these patterns with a 3-year, circumpolar study of ...
Environmental Sciences
Derivation of burn scar depths and estimation of carbon emissions with LIDAR in Indonesian peatlands
During the 1997/98 El Niño-induced drought peatland fires in Indonesia may have released
13–40% of the mean annual global carbon emissions from fossil fuels. One major unknown
in current peatland emission estimations is how much peat is combusted by fire. ...
Bacterial alkaline phosphatases (APases) are important enzymes in organophosphate
utilization in the ocean. The subcellular localization of APases has significant ecological
implications for marine biota but is largely unknown. The extensive metagenomic ...
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New insights into bacterial acquisition of phosphorus in the surface ocean
Evolution
In contrast with speciation in terrestrial organisms, marine plankton frequently display
gradual morphological change without lineage division (e.g., phyletic gradualism or
gradual evolution), which has raised the possibility that a different mode of ...
Due to its numerous environmental extremes, the Tibetan Plateau—the world's highest
plateau—is one of the most challenging areas of modern human settlement. Archaeological
evidence dates the earliest settlement on the plateau to the Late Paleolithic, ...
Ants are a dominant feature of terrestrial ecosystems, yet we know little about the
forces that drive their evolution. Recent findings illustrate that their diets range
from herbivorous to predaceous, with “herbivores” feeding primarily on exudates from
...
Several human genetic disorders of hemoglobin have risen in frequency because of the
protection they offer against death from malaria, sickle-cell anemia being a canonical
example. Here we address the issue of why this highly protective mutant, present at
...
Odorant receptors are among the fastest evolving genes in animals. However, little
is known about the functional changes of individual odorant receptors during evolution.
We have recently demonstrated a link between the in vitro function of a human ...
Genetics
The evolutionarily conserved Smc5/6 complex is implicated in recombinational repair,
but its function in this process has been elusive. Here we report that the budding
yeast Smc5/6 complex directly binds to the DNA helicase Mph1. Mph1 and its helicase
...
A new class of small RNAs (endo-siRNAs) produced from endogenous double-stranded RNA
(dsRNA) precursors was recently shown to mediate transposable element (TE) silencing
in the Drosophila soma. These endo-siRNAs might play a role in heterochromatin ...
Immunology
Although, vascular remodeling is a hallmark of many chronic inflammatory disorders such as
rheumatoid arthritis, inflammatory bowel disease, and psoriasis, anti-vascular strategies
to treat these conditions have received little attention to date. We ...
Insect hemocytes mediate important cellular immune responses including phagocytosis
and encapsulation and also secrete immune factors such as opsonins, melanization factors,
and antimicrobial peptides. However, the molecular composition of these important
...
Medical Sciences
Long-term survival of renal allografts depends on the chronic immune response and
is probably influenced by the initial injury caused by ischemia and reperfusion. Hypoxia-inducible
transcription factors (HIFs) are essential for adaptation to low oxygen. ...
In response to DNA damage, checkpoint proteins halt cell cycle progression and promote
repair or apoptosis, thereby preventing mutation accumulation and suppressing tumor
development. The DNA damage checkpoint protein Hus1 associates with Rad9 and Rad1
to ...
Heat shock protein 90-α (Hsp90α) is an intracellular molecular chaperone. However,
it can also be secreted with the underlying regulatory mechanism remaining far from
clear. Here we show that the secreted Hsp90α is a C-terminal truncated form and its
...
Although leukotriene B4 (LTB4) is produced in various inflammatory diseases, its functions in bone metabolism remain
unknown. Using mice deficient in the high-affinity LTB4 receptor BLT1, we evaluated the roles of BLT1 in the development of two bone ...
Astrocyte-elevated gene-1 (AEG-1) expression is increased in multiple cancers and
plays a central role in Ha-ras-mediated oncogenesis through the phosphatidylinositol 3-kinase (PI3K)/Akt signaling
pathway. Additionally, overexpression of AEG-1 protects ...
Cancer development is a multistep process, driven by a series of genetic and environmental
alterations, that endows cells with a set of hallmark traits required for tumorigenesis.
It is broadly accepted that growth signal autonomy, the first hallmark of ...
Microbiology
Transmission of influenza viruses into the human population requires surmounting barriers
to cross-species infection. Changes in the influenza polymerase overcome one such
barrier. Viruses isolated from birds generally contain polymerases with the avian-...
The phototrophic bacterium Chloroflexus aurantiacus uses a yet unsolved 3-hydroxypropionate cycle for autotrophic CO2 fixation. It starts from acetyl-CoA, with acetyl-CoA and propionyl-CoA carboxylases
acting as carboxylating enzymes. In a first cycle, (S)...
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The hydroxypropionate pathway of CO2 fixation: Fait accompli
The σ-like factor YvrI and coregulator YvrHa activate transcription from a small set
of conserved promoters in Bacillus subtilis. We report here that these two proteins independently contribute σ-region 2 and σ-region
4 functions to a holoenzyme-promoter ...
Neuroscience
People with whom one is personally acquainted tend to elicit richer and more vivid
memories than people with whom one does not have a personal connection. Recent findings
from neurons in the human medial temporal lobe (MTL) have shown that individual ...
Exploration is a central component of human and animal behavior that has been studied
in rodents for almost a century. The measures used by neuroscientists to characterize
full-blown exploration are limited in exposing the dynamics of the exploratory ...
The ability to hold multiple objects in memory is fundamental to intelligent behavior,
but its neural basis remains poorly understood. It has been suggested that multiple
items may be held in memory by oscillatory activity across neuronal populations, but
...
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Little is known about the proteins that mediate mechanoelectrical transduction, the
process by which acoustic and accelerational stimuli are transformed by hair cells
of the inner ear into electrical signals. In our search for molecules involved in
...
Cyclin-dependent kinase 5 (Cdk5) and its activator p35 are critical for radial migration
and lamination of cortical neurons. However, how this kinase is regulated by extracellular
and intracellular signals during cortical morphogenesis remains unclear. ...
Circadian rhythms in mammals are generated by a negative transcriptional feedback
loop in which PERIOD (PER) is rate-limiting for feedback inhibition. Casein kinases
Iδ and Iε (CKIδ/ε) can regulate temporal abundance/activity of PER by phosphorylation-...
Astrocytes and one of their products, IL-6, not only support neurons but also mediate
inflammation in the brain. Retinoid-related orphan receptor-α (RORα) transcription
factor has related roles, being neuro-protective and, in peripheral tissues, anti-...
The hippocampus and cerebellum are critically involved in trace eyeblink classical
conditioning (EBCC). The mechanisms underlying the hippocampal-cerebellar interaction
during this task are not well-understood, although hippocampal theta (3–7 Hz) ...
Although the perturbation of either the dopaminergic system or brain-derived neurotrophic
factor (BDNF) levels has been linked to important neurological and neuropsychiatric
disorders, there is no known signaling pathway linking these two major players. ...
Myelination requires a massive increase in glial cell membrane synthesis. Here, we
demonstrate that the acute phase of myelin lipid synthesis is regulated by sterol
regulatory element-binding protein (SREBP) cleavage activation protein (SCAP), an
...
Retinal degenerations are a class of neurodegenerative disorders that ultimately lead
to blindness due to the death of retinal photoreceptors. In most cases, death is the
result of long-term exposure to environmental, inflammatory, and genetic insults.
In ...
Abnormalities in NMDA receptor (NMDAR) function have been implicated in schizophrenia.
Here, we show that dysbindin, a schizophrenia-susceptibility gene widely expressed in the forebrain, controls
the surface expression of NMDARs in a subunit-specific ...
Physiology
Peripheral arterial disease (PAD) affects 5 million people in the US and is the primary
cause of limb amputations. Exercise remains the single best intervention for PAD,
in part thought to be mediated by increases in capillary density. How exercise ...
Time of day-dependent variations of immune system parameters are ubiquitous phenomena
in immunology. The circadian clock has been attributed with coordinating these variations
on multiple levels; however, their molecular basis is little understood. Here, ...
Calcium-activated chloride channels (CaCC) with similar hallmark features are present
in many cell types and mediate important physiological functions including epithelial
secretion, sensory signal transduction, and smooth muscle contraction. Having ...
Plant Biology
The plant hormone abscisic acid (ABA) serves as a physiological monitor to assess
the water status of plants and, under drought conditions, induces stomatal pore closure
by activating specific ion channels, such as a slow-anion channel (SLAC1) that, in
...
In response to drought stress the phytohormone ABA (abscisic acid) induces stomatal
closure and, therein, activates guard cell anion channels in a calcium-dependent as
well as-independent manner. Two key components of the ABA signaling pathway are the
...
The ability to switch from skotomorphogenesis to photomorphogenesis is essential for
seedling development and plant survival. Recent studies revealed that COP1 and phytochrome-interacting
factors (PIFs) are key regulators of this transition by repressing ...
Psychological and Cognitive Sciences
Oxytocin, a peptide that functions as both a hormone and neurotransmitter, has broad
influences on social and emotional processing throughout the body and the brain. In
this study, we tested how a polymorphism (rs53576) of the oxytocin receptor relates
to ...
Speech production is one of the most fundamental activities of humans. A core cognitive
operation involved in this skill is the retrieval of words from long-term memory,
that is, from the mental lexicon. In this article, we establish the time course of
...
The biased-competition theory accounts for attentional effects at the single-neuron
level: It predicts that the neuronal response to simultaneously-presented stimuli
is a weighted average of the response to isolated stimuli, and that attention biases
the ...
Systems Biology
In mammals, the circadian oscillator generates approximately 24-h rhythms in feeding
behavior, even under constant environmental conditions. Livers of mice held under
constant darkness exhibit circadian rhythm in abundance in up to 15% of expressed
...
Cover image: Pictured is a composite image of fossil marine plankton foraminifera on the floor of the Atlantic Ocean. Planktonic foraminifera, which accumulate in great abundance in some parts of the seafloor to form “calcareous ooze,” have been the subject of numerous studies on speciation in the fossil record. Pincelli M. Hull and Richard D. Norris find that the morphological similarity between closely related species and the morphometric techniques employed can greatly influence evolutionary interpretations. See the article by Hull and Norris on pages 21224–21229. Image courtesy of Pincelli M. Hull.
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