Table Of Contents Page, PNAS Volume 108, Number 10
This week in PNAS
Letters (Online Only)
Commentaries
QnAs
Physical Sciences
Applied Physical Sciences
Terrorist attacks on transportation networks have traumatized modern societies. With
a single blast, it has become possible to paralyze airline traffic, electric power
supply, ground transportation or Internet communication. How and at which cost can
one ...
Flagellated bacteria can swim within a thin film of fluid that coats a solid surface,
such as agar; this is a means for colony expansion known as swarming. We found that
micrometer-sized bubbles make excellent tracers for the motion of this fluid. The
...
Chemistry
Phytochrome photoreceptors mediate light responses in plants and in many microorganisms.
Here we report studies using 1H–13C magic-angle spinning NMR spectroscopy of the sensor module of cyanobacterial phytochrome
Cph1. Two isoforms of the red-light ...
The CP29 light harvesting complex from green plants is a pigment-protein complex believed
to collect, conduct, and quench electronic excitation energy in photosynthesis. We
have spectroscopically determined the relative angle between electronic transition
...
Observing individual molecules in a complex environment by fluorescence microscopy
is becoming increasingly important in biological and medical research, for which critical
reduction of observation volume is required. Here, we demonstrate the use of ...
Aptamers have emerged as promising molecular probes for in vivo cancer imaging, but
the reported “always-on” aptamer probes remain problematic because of high background
and limited contrast. To address this problem, we designed an activatable aptamer
...
The fidelity of translation selection begins with the base pairing of codon-anticodon
complex between the m-RNA and tRNAs. Binding of cognate and near-cognate tRNAs induces
30S subunit of the ribosome to wrap around the ternary complex, EF-Tu(GTP)aa-tRNA.
...
Understanding the mechanism of protein folding requires a detailed knowledge of the
structural properties of the barriers separating unfolded from native conformations.
The S-peptide from ribonuclease S forms its α-helical structure only upon binding
to ...
Environmental Sciences
Projected increases in aridity throughout the southwestern United States due to anthropogenic
climate change will likely cause reductions in perennial vegetation cover, which leaves
soil surfaces exposed to erosion. Accelerated rates of dust emission from ...
The growth of microbial cultures in the laboratory often is assessed informally with
a quick flick of the wrist: dense suspensions of microorganisms produce translucent
“swirls” when agitated. Here, we rationalize the mechanism behind this phenomenon
and ...
Geology
Carbonate mud is a major constituent of recent marine carbonate sediments and of ancient
limestones, which contain unique records of changes in ocean chemistry and climate
shifts in the geological past. However, the origin of carbonate mud is ...
We present a 6,000-yr record of changing water balance in the Pacific Northwest inferred
from measurements of carbonate δ18O and grayscale on a sediment core collected from Castor Lake, Washington. This subdecadally
resolved drought record tracks the 1,...
A rise in atmospheric O2 has been linked to the Cambrian explosion of life. For the plankton and animal radiation
that began some 40 million yr later and continued through much of the Ordovician (Great
Ordovician Biodiversification Event), the search for ...
Social Sciences
Anthropology
A large and varied avifaunal bone assemblage from the final Mousterian levels of Grotta
di Fumane, northern Italy, reveals unusual human modifications on species that are
not clearly relatable to feeding or utilitarian uses (i.e., lammergeier, Eurasian
...
Psychological And Cognitive Sciences
How can we concentrate on relevant sounds in noisy environments? A “gain model” suggests
that auditory attention simply amplifies relevant and suppresses irrelevant afferent
inputs. However, it is unclear whether this suffices when attended and ignored ...
Agricultural Sciences
The migratory locust, Locusta migratoria, shows a striking phenotypic plasticity. It transitions between solitary and gregarious
phases in response to population density changes. However, the molecular mechanism
underlying the phase-dependent behavior ...
Anthropology
A large and varied avifaunal bone assemblage from the final Mousterian levels of Grotta
di Fumane, northern Italy, reveals unusual human modifications on species that are
not clearly relatable to feeding or utilitarian uses (i.e., lammergeier, Eurasian
...
Applied Biological Sciences
Observing individual molecules in a complex environment by fluorescence microscopy
is becoming increasingly important in biological and medical research, for which critical
reduction of observation volume is required. Here, we demonstrate the use of ...
Aptamers have emerged as promising molecular probes for in vivo cancer imaging, but
the reported “always-on” aptamer probes remain problematic because of high background
and limited contrast. To address this problem, we designed an activatable aptamer
...
Biochemistry
Recent studies of several key developmental transitions have brought into question
the long held view of the basal transcriptional apparatus as ubiquitous and invariant.
In an effort to better understand the role of core promoter recognition and ...
Cyclodipeptides are secondary metabolites biosynthesized by many bacteria and exhibit
a wide array of biological activities. Recently, a new class of small proteins, named
cyclodipeptide synthases (CDPS), which are unrelated to the typical nonribosomal ...
Mitochondria have their own translational machineries for the synthesis of thirteen
polypeptide chains that are components of the complexes that participate in the process
of oxidative phosphorylation (or ATP generation). Translation initiation in ...
ATP is synthesized by ATP synthase (FOF1-ATPase). Its rotary electromotor (FO) translocates protons (in some organisms sodium cations) and generates torque to
drive the rotary chemical generator (F1). Elastic power transmission between FO and F1 is ...
RlmN and Cfr are Radical SAM enzymes that modify a single adenosine nucleotide—A2503—in
23S ribosomal RNA. This nucleotide is positioned within the peptidyl transferase center
of the ribosome, which is a target of numerous antibiotics. An unusual feature ...
Transporters of the amino acid, polyamine and organocation (APC) superfamily play
essential roles in cell redox balance, cancer, and aminoacidurias. The bacterial L-arginine/agmatine
antiporter, AdiC, is the main APC structural paradigm and shares the “5 +...
Hydrogenases catalyze the reversible reaction 2H+ + 2e-↔H2 with an equilibrium constant that is dependent on the reducing potential of electrons
carried by their redox partner. To examine the possibility of increasing the photobiological
production of ...
Biophysics And Computational Biology
Phytochrome photoreceptors mediate light responses in plants and in many microorganisms.
Here we report studies using 1H–13C magic-angle spinning NMR spectroscopy of the sensor module of cyanobacterial phytochrome
Cph1. Two isoforms of the red-light ...
The CP29 light harvesting complex from green plants is a pigment-protein complex believed
to collect, conduct, and quench electronic excitation energy in photosynthesis. We
have spectroscopically determined the relative angle between electronic transition
...
The fidelity of translation selection begins with the base pairing of codon-anticodon
complex between the m-RNA and tRNAs. Binding of cognate and near-cognate tRNAs induces
30S subunit of the ribosome to wrap around the ternary complex, EF-Tu(GTP)aa-tRNA.
...
Understanding the mechanism of protein folding requires a detailed knowledge of the
structural properties of the barriers separating unfolded from native conformations.
The S-peptide from ribonuclease S forms its α-helical structure only upon binding
to ...
Membrane fusion is required for diverse biological functions ranging from viral infection
to neurotransmitter release. Fusogenic proteins increase the intrinsically slow rate
of fusion by coupling energetically downhill conformational changes of the ...
View related content:
Cytochrome c oxidase (CcO) is the terminal enzyme of the respiratory chain. This redox-driven proton pump
catalyzes the four-electron reduction of molecular oxygen to water, one of the most
fundamental processes in biology. Elucidation of the intermediate ...
AmtB, a member of the Rh/Amt/MEP superfamily, is responsible for ammonia transport
in Escherichia coli. The ammonia pathway in AmtB consists of a narrow hydrophobic lumen in between hydrophilic
periplasmic and cytoplasmic vestibules. A series of molecular ...
Cell Biology
The generation of the tubular network of the endoplasmic reticulum (ER) requires homotypic
membrane fusion that is mediated by the dynamin-like, membrane-bound GTPase atlastin
(ATL). Here, we have determined crystal structures of the cytosolic segment of ...
Microtubules are integral to neuronal development and function. They endow cells with
polarity, shape, and structure, and their extensive surface area provides substrates
for intracellular trafficking and scaffolds for signaling molecules. Consequently,
...
Microtubule plus-end-tracking proteins (+TIPs) localize to growing microtubule plus
ends to regulate a multitude of essential microtubule functions. End-binding proteins
(EBs) form the core of this network by recognizing a distinct structural feature ...
Ipl1/Aurora B is the catalytic subunit of a complex that is required for chromosome
segregation and nuclear division. Before anaphase, Ipl1 localizes to kinetochores,
where it is required to establish proper kinetochore–microtubule associations and
...
Epithelia are planar tissues that undergo major morphogenetic movements during development.
These movements must work in the context of the mechanical properties of epithelia.
Surprisingly little is known about these mechanical properties at the time and ...
Developmental Biology
We report that the dominant human missense mutations G303E and G296S in GATA4, a cardiac-specific transcription factor gene, cause atrioventricular septal defects
and valve abnormalities by disrupting a signaling cascade involved in endocardial
cushion ...
The mammalian fetus represents a semiallograft within the maternal uterus yet is not
rejected. This situation is particularly pronounced in species with a hemochorial
type of placentation, such as humans and rodents, where maternal tissues and blood
are ...
View related content:
Strangers no more: Uterine NK cell recognition of the placenta in mice
Somites form along the embryonic axis by sequential segmentation from the presomitic
mesoderm (PSM) and differentiate into the segmented vertebral column as well as other
unsegmented tissues. Somites are thought to form via the intersection of two ...
Ecology
The extinction of a species is inevitably preceded by the extirpation of a series
of local populations. Ecological theory predicts that vulnerability to extirpation
varies between populations and is ultimately linked to environmental heterogeneity.
If ...
Chain formation is common among phytoplankton organisms but the underlying reasons
and consequences are poorly understood. Here we show that chain formation is strongly
impaired by waterborne cues from copepod grazers in the dinoflagellate Alexandrium ...
Environmental Sciences
Diatoms are responsible for a large fraction of CO2 export to deep seawater, a process responsible for low modern-day CO2 concentrations in surface seawater and the atmosphere. Like other photosynthetic
organisms, diatoms have adapted to these low ambient ...
A principle response of C3 plants to increasing concentrations of atmospheric CO2 (CO2) is to reduce transpirational water loss by decreasing stomatal conductance (gs) and simultaneously increase assimilation rates. Via this adaptation, vegetation
has the ...
Plant physiological adaptation to the global rise in atmospheric CO2 concentration (CO2) is identified as a crucial climatic forcing. To optimize functioning under rising
CO2, plants reduce the diffusive stomatal conductance of their leaves (gs) ...
Evolution
Why is motility so common in bacteria? An obvious answer to this ecological and evolutionary
question is that in almost all habitats, bacteria need to go someplace and particularly
in the direction of food. Although the machinery required for motility and ...
The obligate mutualism between leafcutter ants and their Attamyces fungi originated 8 to 12 million years ago in the tropics, but extends today also
into temperate regions in South and North America. The northernmost leafcutter ant
Atta texana sustains ...
Bird beaks display tremendous variation in shape and size, which is closely associated
with the exploitation of multiple ecological niches and likely played a key role in
the diversification of thousands of avian species. Previous studies have ...
Genetics
Variable expressivity of mutant phenotypes in genetically identical individuals is
a phenomenon widely reported but poorly understood. For example, mutations in the
gene encoding the transcription factor ALR-1 in Caenorhabditis elegans result in variable ...
Ancient tetraploidies are found throughout the eukaryotes. After duplication, one
copy of each duplicate gene pair tends to be lost (fractionate). For all studied tetraploidies,
the loss of duplicated genes, known as homeologs, homoeologs, ohnologs, or ...
Immunology
Claudins (Clds) are crucial constituents of tight-junction strands in epithelial cells
and have a central role in barrier functions. We show that Cld4 is unexpectedly expressed
in normal thymic lymphocytes independently of tight junctions. The Cld4 ...
The stimulatory natural killer group 2 member D (NKG2D) lymphocyte receptor and its
tumor-associated ligands are important mediators in the immune surveillance of cancer.
With advanced human tumors, however, persistent NKG2D ligand expression may favor
...
Pertussis is a highly contagious respiratory disease that is especially dangerous
for infants and children. Despite mass vaccination, reported pertussis cases have
increased in the United States and other parts of the world, probably because of increased
...
A wide variety of human cancers are associated with injury. Although stem cells participate
in tissue regeneration after wounding, it is unclear whether these cells also contribute
to epithelial tumors. Human basal cell carcinomas (BCCs) are associated ...
Chronic wounds and acute trauma constitute well-established risk factors for development
of epithelial-derived skin tumors, although the underlying mechanisms are largely
unknown. Basal cell carcinomas (BCCs) are the most common skin cancers displaying
a ...
This article has a correction:
Geldanamycin and its derivative 17AAG [17-(Allylamino)-17-demethoxygeldanamycin, telatinib]
bind selectively to the Hsp90 chaperone protein and inhibit its function. We discovered
that these drugs associate with mitochondria, specifically to the ...
In peripheral target tissues, levels of active glucocorticoid hormones are controlled
by 11β-hydroxysteroid dehydrogenase type 1 (11β-HSD1), a dimeric enzyme that catalyzes
the reduction of cortisone to cortisol within the endoplasmic reticulum. Loss of ...
Chemotherapy-induced broad toxicities are the leading cause of the drug-induced mortality
in cancer patients. Antiangiogenic drugs (ADs) in combination with chemotherapy are
widely used as front-line therapy for the treatment of various human cancers. ...
Histone deacetylases (HDACs) regulate cardiac plasticity; however, their molecular
targets are unknown. As autophagy contributes to pathological cardiac remodeling,
we hypothesized that HDAC inhibitors target autophagy. The prototypical HDAC inhibitor
(...
Although aerobic glycolysis (the Warburg effect) is a hallmark of cancer, key questions,
including when, how, and why cancer cells become highly glycolytic, remain less clear.
For a largely unknown regulatory mechanism, a rate-limiting glycolytic enzyme ...
A causal role for mitochondrial DNA (mtDNA) mutagenesis in mammalian aging is supported
by recent studies demonstrating that the mtDNA mutator mouse, harboring a defect in
the proofreading-exonuclease activity of mitochondrial polymerase gamma, exhibits
...
This article has an expression of concern:
Histone deacetylase inhibitors (HDACi) have been successfully used as monotherapies
for the treatment of hematological malignancies; however, the single agent effects
of HDACi against solid tumors are less robust. Using preclinical models of lymphoma,
we ...
Microbiology
Flagellated bacteria can swim within a thin film of fluid that coats a solid surface,
such as agar; this is a means for colony expansion known as swarming. We found that
micrometer-sized bubbles make excellent tracers for the motion of this fluid. The
...
Microbes in nature frequently function as members of complex multitaxon communities,
but the structural organization of these communities at the micrometer level is poorly
understood because of limitations in labeling and imaging technology. We report ...
Anaerobic digestion is the most successful bioenergy technology worldwide with, at
its core, undefined microbial communities that have poorly understood dynamics. Here,
we investigated the relationships of bacterial community structure (>400,000 16S rRNA
...
H9N2 influenza viruses have been circulating worldwide in multiple avian species and
repeatedly infecting mammals, including pigs and humans, posing a significant threat
to public health. The coexistence of H9N2 and pandemic influenza H1N1/2009 viruses
in ...
Ammonia oxidation is an essential part of the global nitrogen cycling and was long
thought to be driven only by bacteria. Recent findings expanded this pathway also
to the archaea. However, most questions concerning the metabolism of ammonia-oxidizing
...
It is often assumed that antibiotics act on the most vulnerable cellular targets,
particularly those that require limited inhibition to block growth. To evaluate this
assumption, we developed a genetic method that can inducibly deplete targeted proteins
...
Neuroscience
How can we concentrate on relevant sounds in noisy environments? A “gain model” suggests
that auditory attention simply amplifies relevant and suppresses irrelevant afferent
inputs. However, it is unclear whether this suffices when attended and ignored ...
The cortical output layer 5 contains two excitatory cell types, slender- and thick-tufted
neurons. In rat vibrissal cortex, slender-tufted neurons carry motion and phase information
during active whisking, but remain inactive after passive whisker touch. ...
The aggregation of proteins into oligomers and amyloid fibrils is characteristic of
several neurodegenerative diseases, including Parkinson disease (PD). In PD, the process
of aggregation of α-synuclein (α-syn) from monomers, via oligomeric intermediates,
...
Despite ubiquitous expression and a high level of metastasis-associated protein 1
(MTA1) coregulator, the physiological role of the MTA1 coactivator remains unknown.
We found that MTA1 is a bona fide coactivator and stimulator of tyrosine hydroxylase
(TH) ...
Signaling through N-methyl-d-aspartate–type glutamate receptors (NMDARs) is essential for the development of behavioral
sensitization to psychostimulants such as amphetamine (AMPH). However, the cell type
and brain region in which NMDAR signaling is ...
Fetal exposure to environmental insults increases the susceptibility to late-onset
neuropsychiatric disorders. Alcohol is listed as one of such prenatal environmental
risk factors and known to exert devastating teratogenetic effects on the developing
...
We report on a secreted protein found in mammalian cochlear outer hair cells (OHC)
that is a member of the carcinoembryonic antigen-related cell adhesion molecule (CEACAM)
family of adhesion proteins. Ceacam16 mRNA is expressed in OHC, and its protein ...
The compound eye of insects imposes a tradeoff between resolution and sensitivity,
which should exacerbate with diminishing eye size. Tiny lenses are thought to deliver
poor acuity because of diffraction; nevertheless, miniature insects have visual ...
It has been suggested that the frontal operculum (fO) is a key node in a network for
exerting control over cognitive processes. How it exerts this influence, however,
has been unclear. Here, using the complementary approaches of functional MRI and ...
Apolipoprotein (apo) E4 is the major known genetic risk factor for Alzheimer's disease
(AD). We have shown in vitro and in vivo that apoE4 preferentially undergoes aberrant
cleavage in neurons, yielding neurotoxic C-terminal-truncated fragments. To study
...
Although some DNA methylation patterns are altered by steroid hormone exposure in
the developing brain, less is known about how changes in steroid hormone levels influence
DNA methylation patterns in the adult brain. Steroid hormones act in the adult ...
Physiology
Carbonate mud is a major constituent of recent marine carbonate sediments and of ancient
limestones, which contain unique records of changes in ocean chemistry and climate
shifts in the geological past. However, the origin of carbonate mud is ...
Plant Biology
A fundamental aspect of climate change is the potential shifts in flowering phenology
and pollen initiation associated with milder winters and warmer seasonal air temperature.
Earlier floral anthesis has been suggested, in turn, to have a role in human ...
Population Biology
This paper presents research on the genetic structure and diversity of populations
of a common marine protist and their changes over time. The bloom-forming diatom Skeletonema marinoi was used as a model organism. Strains were revived from anoxic discrete ...
View related content:
Cryptic planktonic diatom challenges phytoplankton ecologists
Systems Biology
How do living cells achieve sufficient abundances of functional protein complexes
while minimizing promiscuous nonfunctional interactions? Here we study this problem
using a first-principle model of the cell whose phenotypic traits are directly determined
...
Corrections
Cover image: Pictured is an electron microscopy image of the diatom�Skeletonema, a globally occurring marine organism that constitutes a valuable food source for marine animals. Karolina Härnström et al. tracked the genetic structure of a Skeletonema marinoi population within Danish fjord sediments that had accumulated over 100 years, and found that the population’s genetic structure changed little over thousands of generations and did not mix with diatom populations from the open sea, despite constant water exchange. See the article by Härnström et al. on pages 4252–4257. Image courtesy of Lars Edler (WEAQ AB, Sweden) and Gustaaf Hallegraeff (University of Tasmania, Hobart, Tasmania, Australia).
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