Table Of Contents Page, PNAS Volume 106, Number 43
This Week in PNAS
Letters (Online Only)
Editorial
Commentaries
Profile
Plant and Insect Biodiversity Special Feature (free online)
Perspective
Terrestrial biodiversity is dominated by plants and the herbivores that consume them,
and they are one of the major conduits of energy flow up to higher trophic levels.
Here, we address the processes that have generated the spectacular diversity of ...
Research Articles
A central paradigm in the field of plant–herbivore interactions is that the diversity
and complexity of secondary compounds in plants have intensified over evolutionary
time, resulting in the great variety of secondary products that currently exists.
...
One signature of adaptive radiation is a high level of trait change early during the
diversification process and a plateau toward the end of the radiation. Although the
study of the tempo of evolution has historically been the domain of paleontologists,
...
Plants and their herbivores constitute more than half of the organisms in tropical
forests. Therefore, a better understanding of the evolution of plant defenses against
their herbivores may be central for our understanding of tropical biodiversity. Here,
...
Despite the importance of plant–herbivore interactions to the ecology and evolution
of terrestrial ecosystems, the evolutionary factors contributing to variation in plant
defenses against herbivores remain unresolved. We used a comparative phylogenetic
...
We conducted phylogenetically informed comparative analyses of 81 taxa of Dalechampia (Euphorbiaceae) vines and shrubs to assess the roles of historical contingency and
trait interaction in the evolution of plant-defense and pollinator-attraction systems.
...
Ant-plant interactions represent a diversity of strategies, from exploitative to mutualistic,
and how these strategies evolve is poorly understood. Here, we link physiological,
ecological, and phylogenetic approaches to study the evolution and coexistence ...
Introduced plants tend to experience less herbivory than natives, although herbivore
loads vary widely. Herbivores may switch hosts onto an introduced plant for at least
two reasons. They may recognize the novel plant as a potential host based on ...
A central but little-tested prediction of “escape and radiation” coevolution is that
colonization of novel, chemically defended host plant clades accelerates insect herbivore
diversification. That theory, in turn, exemplifies one side of a broader debate ...
Physical Sciences
Applied Mathematics
The bacterium Bacillus subtilis produces the molecule surfactin, which is known to enhance the spreading of multicellular
colonies on nutrient substrates by lowering the surface tension of the surrounding
fluid, and to aid in the formation of aerial ...
Many nosocomial outbreaks exhibit “superspreading events” in which cross-transmission
occurs via a single individual to a large number of patients. We investigated how
heterogeneity in Health-Care Worker (HCW) behaviors, especially compliance to hand
...
Chemistry
Crystallography and computer modeling have been used to exploit a previously unexplored
channel in the glucocorticoid receptor (GR). Highly potent, nonsteroidal indazole
amides showing excellent complementarity to the channel were designed with the ...
Molecular scale signal conversion and multiplication is of particular importance in
many physical and biological applications, such as molecular switches, nano-gates,
biosensors, and various neural systems. Unfortunately, little is currently known ...
DNA hybridization plays a central role in biology and, increasingly, in materials
science. Yet, there is no precedent for examining the pathways by which specific single-stranded
DNA sequences interact to assemble into a double helix. A detailed model of ...
This article has a correction:
Metabolic fluxes can serve as specific biomarkers for detecting malignant transformations,
tumor progression, and response to microenvironmental changes and treatment procedures.
We present noninvasive hyperpolarized 13C NMR investigations on the ...
Recent cases of avian influenza H5N1 and the swine-origin 2009 H1N1 have caused a
great concern that a global disaster like the 1918 influenza pandemic may occur again.
Viral transmission begins with a critical interaction between hemagglutinin (HA) ...
Establishing mechanisms and intrinsic reactivity in the oxidation of phenol with water
as the proton acceptor is a fundamental task relevant to many reactions occurring
in natural systems. Thanks to the easy measure of the reaction kinetics by the current
...
Staphylococcus aureus CzrA is a zinc-dependent transcriptional repressor from the ubiquitous ArsR family
of metal sensor proteins. Zn(II) binds to a pair of intersubunit C-terminal α5-sensing
sites, some 15 Å distant from the DNA-binding interface, and ...
Computer Sciences
Very realistic human-looking robots or computer avatars tend to elicit negative feelings
in human observers. This phenomenon is known as the “uncanny valley” response. It
is hypothesized that this uncanny feeling is because the realistic synthetic ...
Engineering
Cells within a genetically identical population exhibit phenotypic variation that
in some cases can persist across multiple generations. However, information about
the temporal variation and familial dependence of protein levels remains hidden when
...
Geology
Based on elevated concentrations of a set of “impact markers” at the onset of the
Younger Dryas stadial from sedimentary contexts across North America, Firestone, Kennett,
West, and others have argued that 12.9 ka the Earth experienced an impact by an ...
Social Sciences
Anthropology
Based on elevated concentrations of a set of “impact markers” at the onset of the
Younger Dryas stadial from sedimentary contexts across North America, Firestone, Kennett,
West, and others have argued that 12.9 ka the Earth experienced an impact by an ...
Biological Sciences
Agricultural Sciences
Consensus genetic linkage maps provide a genomic framework for quantitative trait
loci identification, map-based cloning, assessment of genetic diversity, association
mapping, and applied breeding in marker-assisted selection schemes. Among “orphan
crops” ...
Anthropology
Although the molecular clock hypothesis posits that the rate of molecular change is
constant over time, there is evidence that rates vary among lineages. Some of the
strongest evidence for variable molecular rates comes from the primates; e.g., the
“...
Applied Biological Sciences
Crystallography and computer modeling have been used to exploit a previously unexplored
channel in the glucocorticoid receptor (GR). Highly potent, nonsteroidal indazole
amides showing excellent complementarity to the channel were designed with the ...
Insect transgenesis is mainly based on the random genomic integration of DNA fragments
embedded into non-autonomous transposable elements. Once a random insertion into a
specific location of the genome has been identified as particularly useful with ...
Biochemistry
Staphylococcus aureus CzrA is a zinc-dependent transcriptional repressor from the ubiquitous ArsR family
of metal sensor proteins. Zn(II) binds to a pair of intersubunit C-terminal α5-sensing
sites, some 15 Å distant from the DNA-binding interface, and ...
Deinococcus radiodurans (Dr) withstands desiccation, reactive oxygen species, and doses of radiation that
would be lethal to most organisms. Deletion of a gene encoding a homolog of mammalian
nitric oxide synthase (NOS) severely compromises the recovery ...
Mobile group II introns retrohome by an RNP-based mechanism in which the excised intron
lariat RNA fully reverse splices into a DNA site via 2 sequential transesterification
reactions and is reverse transcribed by the associated intron-encoded protein. ...
A macromolecular X-ray crystal structure is usually represented as a single static
model with a single set of temperature factors representing a simple approximation
of motion and disorder of the structure. Multiconformer representations of small proteins
...
Reactive oxygen species (ROS) interact with DNA, frequently generating highly mutagenic
7,8-dihydro-8-oxoguanine (8-oxo-G) lesions. Replicative DNA polymerases (pols) often
misincorporate adenine opposite 8-oxo-G. The subsequent repair mechanism allowing
...
The kinetics and magnitude of cytokine gene expression are tightly regulated to elicit
a balanced response to pathogens and result from integrated changes in transcription
and mRNA stability. Yet, how a single microbial stimulus induces peak transcription
...
Ubiquitination by the anaphase-promoting complex (APC/C) is essential for proliferation
in all eukaryotes. The human APC/C promotes the degradation of mitotic regulators
by assembling K11-linked ubiquitin chains, the formation of which is initiated by
its ...
Cyclobutane pyrimidine dimers (CPDs) constitute the most frequent UV-induced DNA photoproduct.
However, it has remained unclear how human and other mammalian cells mitigate the
mutagenic and carcinogenic potential of CPDs emanating from their replicative ...
We report the X-ray crystal structure of a phosphodiesterase (PDE) that includes both
catalytic and regulatory domains. PDE2A (215–900) crystallized as a dimer in which
each subunit had an extended organization of regulatory GAF-A and GAF-B and catalytic
...
Biophysics and Computational Biology
Molecular scale signal conversion and multiplication is of particular importance in
many physical and biological applications, such as molecular switches, nano-gates,
biosensors, and various neural systems. Unfortunately, little is currently known ...
DNA hybridization plays a central role in biology and, increasingly, in materials
science. Yet, there is no precedent for examining the pathways by which specific single-stranded
DNA sequences interact to assemble into a double helix. A detailed model of ...
This article has a correction:
Metabolic fluxes can serve as specific biomarkers for detecting malignant transformations,
tumor progression, and response to microenvironmental changes and treatment procedures.
We present noninvasive hyperpolarized 13C NMR investigations on the ...
Single-molecule manipulation studies have revealed that double-stranded DNA undergoes
a structural transition when subjected to tension. At forces that depend on the attachment
geometry of the DNA (65 pN or 110 pN), it elongates ≈1.7-fold and its elastic ...
View related content:
Hexameric ring-shaped AAA+ molecular motors have a key function of active translocation
of a macromolecular chain through the central pore. By performing multiscale molecular
dynamics (MD) simulations, we revealed that HslU, a AAA+ motor in a bacterial ...
Living cells sense the rigidity of their environment and adapt their activity to it.
In particular, cells cultured on elastic substrates align their shape and their traction
forces along the direction of highest stiffness and preferably migrate towards ...
Structure–function relationships in proteins are predicated on the spatial proximity
of noncovalently interacting groups of atoms. Thus, structural elements located away
from a protein's active site are typically presumed to serve a stabilizing or ...
We simultaneously measure both the step size, via FIONA, and the 3-D orientation,
via DOPI, of the light-chain domain of individual dimeric myosin VIs. This allows
for the correlation of the change in orientation of the light chain domain to the
stepping ...
A rigorous numerical test of a hypothetical mechanism of a molecular motor should
model explicitly the diffusive motion of the motor's degrees of freedom as well as
the transition rates between the motor's chemical states. We present such a Brownian
...
Rather than maximizing toughness, as needed for silk and muscle titin fibers to withstand
external impact, the much softer extracellular matrix fibers made from fibronectin
(Fn) can be stretched by cell generated forces and display extraordinary ...
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease linked to the misfolding
of Cu/Zn superoxide dismutase (SOD1). ALS-related defects in SOD1 result in a gain
of toxic function that coincides with aberrant oligomerization. The structural ...
Cell Biology
Cells within a genetically identical population exhibit phenotypic variation that
in some cases can persist across multiple generations. However, information about
the temporal variation and familial dependence of protein levels remains hidden when
...
The proinflammatory cytokine TNF-α exerts its pleiotropic functions through activation
of multiple downstream effectors, including JNK1. Yet, the underlying regulatory mechanism
is incompletely understood. Here, we report that the transcription factor Myc-...
Statins are compounds prescribed to lower blood cholesterol in millions of patients
worldwide. They act by inhibiting HMG-CoA reductase, the rate-limiting enzyme in the
mevalonate pathway that leads to the synthesis of farnesyl pyrophosphate, a precursor
...
Developmental Biology
Design features that ensure reproducible and invariant embryonic processes are major
characteristics of current gene regulatory network models. New cis-regulatory studies on a gene regulatory network subcircuit activated early in the
development of the ...
We conducted a genetic analysis of the developing temporo-mandibular or temporomandi-bular
joint (TMJ), a highly specialized synovial joint that permits movement and function
of the mammalian jaw. First, we used laser capture microdissection to perform a ...
This article has a correction:
Using a proteomics screen, we have identified the methyltransferase G9a as an interacting
partner of the hematopoietic activator NF-E2. We show that G9a is recruited to the
β-globin locus in a NF-E2-dependent manner and spreads over the entire locus. ...
Tail resorption during amphibian metamorphosis has been thought to be controlled mainly
by a cell-autonomous mechanism of programmed cell death triggered by thyroid hormone.
However, we have proposed a role for the immune response in metamorphosis, based ...
Ecology
Ant-plant interactions represent a diversity of strategies, from exploitative to mutualistic,
and how these strategies evolve is poorly understood. Here, we link physiological,
ecological, and phylogenetic approaches to study the evolution and coexistence ...
Periglacial soils are one of the least studied ecosystems on Earth, yet they are widespread
and are increasing in area due to retreat of glaciers worldwide. Soils in these environments
are cold and during the brief summer are exposed to high levels of UV ...
Evolution
A central paradigm in the field of plant–herbivore interactions is that the diversity
and complexity of secondary compounds in plants have intensified over evolutionary
time, resulting in the great variety of secondary products that currently exists.
...
One signature of adaptive radiation is a high level of trait change early during the
diversification process and a plateau toward the end of the radiation. Although the
study of the tempo of evolution has historically been the domain of paleontologists,
...
Plants and their herbivores constitute more than half of the organisms in tropical
forests. Therefore, a better understanding of the evolution of plant defenses against
their herbivores may be central for our understanding of tropical biodiversity. Here,
...
Despite the importance of plant–herbivore interactions to the ecology and evolution
of terrestrial ecosystems, the evolutionary factors contributing to variation in plant
defenses against herbivores remain unresolved. We used a comparative phylogenetic
...
We conducted phylogenetically informed comparative analyses of 81 taxa of Dalechampia (Euphorbiaceae) vines and shrubs to assess the roles of historical contingency and
trait interaction in the evolution of plant-defense and pollinator-attraction systems.
...
Introduced plants tend to experience less herbivory than natives, although herbivore
loads vary widely. Herbivores may switch hosts onto an introduced plant for at least
two reasons. They may recognize the novel plant as a potential host based on ...
A central but little-tested prediction of “escape and radiation” coevolution is that
colonization of novel, chemically defended host plant clades accelerates insect herbivore
diversification. That theory, in turn, exemplifies one side of a broader debate ...
Genetics
The identification of specific functional roles for the numerous long noncoding (nc)RNAs
found in eukaryotic transcriptomes is currently a matter of intense study amid speculation
that these ncRNAs have key regulatory roles. We have identified a pair of ...
View related content:
Immunology
Recent cases of avian influenza H5N1 and the swine-origin 2009 H1N1 have caused a
great concern that a global disaster like the 1918 influenza pandemic may occur again.
Viral transmission begins with a critical interaction between hemagglutinin (HA) ...
IL-10 produced by dendritic cells (DC) can limit or terminate ongoing inflammatory
responses by inhibiting the proinflammatory cytokine production. Currently, the molecular
mechanism by which IL-10 suppresses cytokine production is still ill-defined. In ...
With age, T-cell generation from the thymus is much reduced, yet a substantial naïve
T-cell pool is maintained even in aged animals, suggesting that naïve T cells either
persist longer or turn over faster to maintain T-cell homeostasis. We found that with
...
Canonical chromosomal translocations juxtaposing antigen receptor genes and oncogenes
are a hallmark of many lymphoid malignancies. These translocations frequently form
through the joining of DNA ends from double-strand breaks (DSBs) generated by the
...
The activity of integrin LFA-1 (αLβ2) to its ligand ICAM-1 is regulated through the conformational changes of its ligand-binding
domain, the I domain of αL chain, from an inactive, low-affinity closed form (LA), to an intermediate-affinity
form (IA), and ...
Medical Sciences
In cancer, genetically activated proto-oncogenes often induce “upstream” dependency on the activity of the mutant oncoprotein. Therapeutic inhibition of
these activated oncoproteins can induce massive apoptosis of tumor cells, leading
to sometimes ...
Genome-wide studies reveal that transcription by RNA polymerase II (Pol II) is dynamically
regulated. To obtain a comprehensive view of a single transcription cycle, we switched
on transcription of five long human genes (>100 kbp) with tumor necrosis ...
Microbiology
The bacterium Bacillus subtilis produces the molecule surfactin, which is known to enhance the spreading of multicellular
colonies on nutrient substrates by lowering the surface tension of the surrounding
fluid, and to aid in the formation of aerial ...
Neuroscience
Very realistic human-looking robots or computer avatars tend to elicit negative feelings
in human observers. This phenomenon is known as the “uncanny valley” response. It
is hypothesized that this uncanny feeling is because the realistic synthetic ...
The hypothesis that amyloid-β (Aβ) peptides are the primary cause of Alzheimer's disease
(AD) remains the best supported theory of AD pathogenesis. Yet, many observations
are inconsistent with the hypothesis. Aβ peptides are generated when amyloid ...
A critical step in synapse formation is the clustering of neurotransmitter receptors
in the postsynaptic membrane, directly opposite the nerve terminal. At the neuromuscular
junction, a widely studied model synapse, acetylcholine receptors (AChRs) ...
We used noninvasive MRI and voxel-based morphometry (VBM) to detect changes in brain
structure in three adult Japanese macaques trained to use a rake to retrieve food
rewards. Monkeys, who were naive to any previous tool use, were scanned repeatedly
in a ...
Short-term synaptic facilitation plays an important role in information processing
in the central nervous system. Although the crucial requirement of presynaptic Ca2+ in the expression of this plasticity has been known for decades, the molecular ...
In functional brain imaging there is controversy over which hemodynamic signal best
represents neural activity. Intrinsic signal optical imaging (ISOI) suggests that
the best signal is the early darkening observed at wavelengths absorbed preferentially
by ...
Pharmacology
The cyclic peptide zyklophin {[N-benzylTyr1,cyclo(D-Asp5,Dap8)-dynorphin A-(1–11)NH2, Patkar KA, et al. (2005) J Med Chem 48: 4500–4503} is a selective peptide kappa opioid receptor (KOR) antagonist that
shows activity following systemic administration. ...
Physiology
The importance of proper ion channel trafficking is underpinned by a number of channel-linked
genetic diseases whose defect is associated with failure to reach the cell surface.
Conceptually, it is reasonable to suggest that the function of ion channels ...
The blood and lymphatic vasculatures are structurally and functionally coupled in
controlling tissue perfusion, extracellular interstitial fluids, and immune surveillance.
Little is known, however, about the molecular mechanisms that underlie the ...
Plant Biology
The plant pathogen Agrobacterium tumefaciens transforms plant cells by delivering its T-DNA into the plant cell nucleus where
it integrates into the plant genome and causes tumor formation. A key role of VirE2-interacting
protein 1 (VIP1) in the nuclear ...
Population Biolgoy
Many nosocomial outbreaks exhibit “superspreading events” in which cross-transmission
occurs via a single individual to a large number of patients. We investigated how
heterogeneity in Health-Care Worker (HCW) behaviors, especially compliance to hand
...
Corrections
Cover image: Pictured is the mural “Oak Family Tree,” from the University of California, Davis, Arboretum's oak collection. The mural, created through the University of California, Davis, Art/Science Fusion program, depicts the evolutionary relationships of 29 oak species and the animals associated with each species. Ian S. Pearse and Andrew L. Hipp report a phylogenetic analysis of native and non-native oaks and seek to understand why insect herbivores interact with some introduced plant species more than others. See the article by Pearse and Hipp, which is part of the Plant and Insect Biodiversity Special Feature, on pages 18097–18102. Image courtesy of Allan Jones (University of California, Davis, CA).
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