bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of a hidden strain switch provides clues to an ancient structural mechanism in protein kinases
Authors: Oruganty Krishnadev , Talathi Nakul Suhas , Wood Zachary A. , Kannan Natarajan
Published: January 2013

The protein kinase catalytic domain contains several conserved residues of unknown functions. Here, using a combination of computational and experimental approaches, we show that the function of some of these residues is to maintain the backbone geometry of the active site in a strained conformation. Specifically, we find that the backbone geometry of the catalytically important HRD motif deviates from ideality in high-resolution structures and the strained geometry results in favorable hydrogen bonds with conserved noncatalytic residues in the active site. In particular, a conserved aspartate in the F-helix hydrogen bonds to the strained HRD backbone in diverse eukaryotic and eukaryotic-like protein kinase crystal structures. Mutations that alter this hydrogen-bonding interaction impair catalytic activity in Aurora kinase. Although the backbone strain is present in most active conformations, several inactive conformations lack the strain because of a peptide flip in the HRD backbone. The peptide flip is correlated with loss of hydrogen bonds with the F-helix aspartate as well as with other interactions associated with kinase regulation. Within protein kinases that are regulated by activation loop phosphorylation, the strained residue is an arginine, which coordinates with the activation loop phosphate. Based on analysis of strain across the protein kinase superfamily, we propose a model in which backbone strain co-evolved with conserved residues for allosteric control of catalytic activity. Our studies provide new clues for the design of allosteric protein kinase inhibitors.
Multidimensional traction force microscopy reveals out-of-plane rotational moments about focal adhesions
Authors: Legant Wesley R. , Choi Colin K. , Miller Jordan S. , Shao Lin , Gao Liang , Betzig Eric , Chen Christopher S.
Published: January 2013

Recent methods have revealed that cells on planar substrates exert both shear (in-plane) and normal (out-of-plane) tractions against the extracellular matrix (ECM). However, the location and origin of the normal tractions with respect to the adhesive and cytoskeletal elements of cells have not been elucidated. We developed a high-spatiotemporal-resolution, multidimensional (2.5D) traction force microscopy to measure and model the full 3D nature of cellular forces on planar 2D surfaces. We show that shear tractions are centered under elongated focal adhesions whereas upward and downward normal tractions are detected on distal (toward the cell edge) and proximal (toward the cell body) ends of adhesions, respectively. Together, these forces produce significant rotational moments about focal adhesions in both protruding and retracting peripheral regions. Temporal 2.5D traction force microscopy analysis of migrating and spreading cells shows that these rotational moments are highly dynamic, propagating outward with the leading edge of the cell. Finally, we developed a finite element model to examine how rotational moments could be generated about focal adhesions in a thin lamella. Our model suggests that rotational moments can be generated largely via shear lag transfer to the underlying ECM from actomyosin contractility applied at the intracellular surface of a rigid adhesion of finite thickness. Together, these data demonstrate and probe the origin of a previously unappreciated multidimensional stress profile associated with adhesions and highlight the importance of new approaches to characterize cellular forces.
Structural basis for Zn
2+
-dependent intercellular adhesion in staphylococcal biofilms
Authors: Conrady Deborah G. , Wilson Jeffrey J. , Herr Andrew B.
Published: January 2013

Significance

Under adverse environmental conditions, bacteria can form specialized antibiotic-resistant colonies called “biofilms.” In
Staphylococcus epidermidis
biofilms, a protein, Aap, links bacterial cells together but does so only in the presence of zinc ions. We have determined the atomic structure of an adhesive portion of Aap bound to zinc. The protein adopts an elongated, flexible fold with zinc ions bridging two protein chains. The mode of assembly indicates that Aap is likely to form twisted rope-like structures between bacterial cells. These data provide clues about regions of the protein that could be targeted to prevent intercellular adhesion in the developing biofilm.
Domain-specific c-Myc ubiquitylation controls c-Myc transcriptional and apoptotic activity
Authors: Zhang Qin , Spears Erick , Boone David N. , Li Zhaoliang , Gregory Mark A. , Hann Stephen R.
Published: January 2013

The oncogenic transcription factor c-Myc causes transformation and tumorigenesis, but it can also induce apoptotic cell death. Although tumor suppressors are necessary for c-Myc to induce apoptosis, the pathways and mechanisms are unclear. To further understand how c-Myc switches from an oncogenic protein to an apoptotic protein, we examined the mechanism of p53-independent c-Myc–induced apoptosis. We show that the tumor suppressor protein ARF mediates this switch by inhibiting ubiquitylation of the c-Myc transcriptional domain (TD). Whereas TD ubiquitylation is critical for c-Myc canonical transcriptional activity and transformation, inhibition of ubiquitylation leads to the induction of the noncanonical c-Myc target gene,
Egr1
, which is essential for efficient c-Myc–induced p53-independent apoptosis. ARF inhibits the interaction of c-Myc with the E3 ubiquitin ligase Skp2. Overexpression of Skp2, which occurs in many human tumors, inhibits the recruitment of ARF to the
Egr1
promoter, leading to inhibition of c-Myc–induced apoptosis. Therapeutic strategies could be developed to activate this intrinsic apoptotic activity of c-Myc to inhibit tumorigenesis.
Tree climbing and human evolution
Authors: Venkataraman Vivek V. , Kraft Thomas S. , Dominy Nathaniel J.
Published: January 2013

Paleoanthropologists have long argued—often contentiously—about the climbing abilities of early hominins and whether a foot adapted to terrestrial bipedalism constrained regular access to trees. However, some modern humans climb tall trees routinely in pursuit of honey, fruit, and game, often without the aid of tools or support systems. Mortality and morbidity associated with facultative arboreality is expected to favor behaviors and anatomies that facilitate safe and efficient climbing. Here we show that Twa hunter–gatherers use extraordinary ankle dorsiflexion (>45°) during climbing, similar to the degree observed in wild chimpanzees. Although we did not detect a skeletal signature of dorsiflexion in museum specimens of climbing hunter–gatherers from the Ituri forest, we did find that climbing by the Twa is associated with longer fibers in the gastrocnemius muscle relative to those of neighboring, nonclimbing agriculturalists. This result suggests that a more excursive calf muscle facilitates climbing with a bipedally adapted ankle and foot by positioning the climber closer to the tree, and it might be among the mechanisms that allow hunter–gatherers to access the canopy safely. Given that we did not find a skeletal correlate for this observed behavior, our results imply that derived aspects of the hominin ankle associated with bipedalism remain compatible with vertical climbing and arboreal resource acquisition. Our findings challenge the persistent arboreal–terrestrial dichotomy that has informed behavioral reconstructions of fossil hominins and highlight the value of using modern humans as models for inferring the limits of hominin arboreality.
Abnormal neuronal patterning occurs during early postnatal brain development of
Scn1b
-null mice and precedes hyperexcitability
Authors: Brackenbury William J. , Yuan Yukun , O’Malley Heather A. , Parent Jack M. , Isom Lori L.
Published: January 2013

Voltage-gated Na
+
channel (VGSC) β1 subunits, encoded by
SCN1B
, are multifunctional channel modulators and cell adhesion molecules (CAMs). Mutations in
SCN1B
are associated with the genetic epilepsy with febrile seizures plus (GEFS+) spectrum disorders in humans, and
Scn1b
-null mice display severe spontaneous seizures and ataxia from postnatal day (P)10. The goal of this study was to determine changes in neuronal pathfinding during early postnatal brain development of
Scn1b
-null mice to test the hypothesis that these CAM-mediated roles of
Scn1b
may contribute to the development of hyperexcitability. c-Fos, a protein induced in response to seizure activity, was up-regulated in the
Scn1b
-null brain at P16 but not at P5. Consistent with this, epileptiform activity was observed in hippocampal and cortical slices prepared from the P16 but not from the P5–P7
Scn1b
-null brain. On the basis of these results, we investigated neuronal pathfinding at P5. We observed disrupted fasciculation of parallel fibers in the P5 null cerebellum. Further, P5 null mice showed reduced neuron density in the dentate gyrus granule cell layer, increased proliferation of granule cell precursors in the hilus, and defective axonal extension and misorientation of somata and processes of inhibitory neurons in the dentate gyrus and CA1. Thus,
Scn1b
is critical for neuronal proliferation, migration, and pathfinding during the critical postnatal period of brain development. We propose that defective neuronal proliferation, migration, and pathfinding in response to
Scn1b
deletion may contribute to the development of hyperexcitability.
Identification of an essential endogenous regulator of blood–brain barrier integrity, and its pathological and therapeutic implications
Authors: Cristante Enrico , McArthur Simon , Mauro Claudio , Maggioli Elisa , Romero Ignacio A. , Wylezinska-Arridge Marzena , Couraud Pierre O. , Lopez-Tremoleda Jordi , Christian Helen C. , Weksler Babette B. , Malaspina Andrea , Solito Egle
Published: January 2013

The blood–brain barrier (BBB), a critical guardian of communication between the periphery and the brain, is frequently compromised in neurological diseases such as multiple sclerosis (MS), resulting in the inappropriate passage of molecules and leukocytes into the brain. Here we show that the glucocorticoid anti-inflammatory messenger annexin A1 (ANXA1) is expressed in brain microvascular endothelial cells, where it regulates BBB integrity. In particular, ANXA1
−/−
mice exhibit significantly increased BBB permeability as a result of disrupted interendothelial cell tight junctions, essentially related to changes in the actin cytoskeleton, which stabilizes tight and adherens junctions. This situation is reminiscent of early MS pathology, a relationship confirmed by our detection of a selective loss of ANXA1 in the plasma and cerebrovascular endothelium of patients with MS. Importantly, this loss is swiftly restored by i.v. administration of human recombinant ANXA1. Analysis in vitro confirms that treatment of cerebrovascular endothelial cells with recombinant ANXA1 restores cell polarity, cytoskeleton integrity, and paracellular permeability through inhibition of the small G protein RhoA. We thus propose ANXA1 as a critical physiological regulator of BBB integrity and suggest it may have utility in the treatment of MS, correcting BBB function and hence ameliorating disease.
Regulating energy transfer of excited carriers and the case for excitation-induced hydrogen dissociation on hydrogenated graphene
Authors: Bang Junhyeok , Meng Sheng , Sun Yi-Yang , West Damien , Wang Zhiguo , Gao Fei , Zhang S. B.
Published: January 2013

Understanding and controlling of excited carrier dynamics is of fundamental and practical importance, particularly in photochemistry and solar energy applications. However, theory of energy relaxation of excited carriers is still in its early stage. Here, using ab initio molecular dynamics (MD) coupled with time-dependent density functional theory, we show a coverage-dependent energy transfer of photoexcited carriers in hydrogenated graphene, giving rise to distinctively different ion dynamics. Graphene with sparsely populated H is difficult to dissociate due to inefficient transfer of the excitation energy into kinetic energy of the H. In contrast, H can easily desorb from fully hydrogenated graphane. The key is to bring down the H antibonding state to the conduction band minimum as the band gap increases. These results can be contrasted to those of standard ground-state MD that predict H in the sparse case should be much less stable than that in fully hydrogenated graphane. Our findings thus signify the importance of carrying out explicit electronic dynamics in excited-state simulations.
Recurrent jellyfish blooms are a consequence of global oscillations
Authors: Condon Robert H. , Duarte Carlos M. , Pitt Kylie A. , Robinson Kelly L. , Lucas Cathy H. , Sutherland Kelly R. , Mianzan Hermes W. , Bogeberg Molly , Purcell Jennifer E. , Decker Mary Beth , Uye Shin-ichi , Madin Laurence P. , Brodeur Richard D. , Haddock Steven H. D. , Malej Alenka , Parry Gregory D. , Eriksen Elena , Quiñones Javier , Acha Marcelo , Harvey Michel , Arthur James M. , Graham William M.
Published: January 2013

A perceived recent increase in global jellyfish abundance has been portrayed as a symptom of degraded oceans. This perception is based primarily on a few case studies and anecdotal evidence, but a formal analysis of global temporal trends in jellyfish populations has been missing. Here, we analyze all available long-term datasets on changes in jellyfish abundance across multiple coastal stations, using linear and logistic mixed models and effect-size analysis to show that there is no robust evidence for a global increase in jellyfish. Although there has been a small linear increase in jellyfish since the 1970s, this trend was unsubstantiated by effect-size analysis that showed no difference in the proportion of increasing vs. decreasing jellyfish populations over all time periods examined. Rather, the strongest nonrandom trend indicated jellyfish populations undergo larger, worldwide oscillations with an approximate 20-y periodicity, including a rising phase during the 1990s that contributed to the perception of a global increase in jellyfish abundance. Sustained monitoring is required over the next decade to elucidate with statistical confidence whether the weak increasing linear trend in jellyfish after 1970 is an actual shift in the baseline or part of an oscillation. Irrespective of the nature of increase, given the potential damage posed by jellyfish blooms to fisheries, tourism, and other human industries, our findings foretell recurrent phases of rise and fall in jellyfish populations that society should be prepared to face.
Environmental perturbations lift the degeneracy of the genetic code to regulate protein levels in bacteria
Authors: Subramaniam Arvind R. , Pan Tao , Cluzel Philippe
Published: January 2013

The genetic code underlying protein synthesis is a canonical example of a degenerate biological system. Degeneracies in physical and biological systems can be lifted by external perturbations, thus allowing degenerate systems to exhibit a wide range of behaviors. Here we show that the degeneracy of the genetic code is lifted by environmental perturbations to regulate protein levels in living cells. By measuring protein synthesis rates from a synthetic reporter library in
Escherichia coli
, we find that environmental perturbations, such as reduction of cognate amino acid supply, lift the degeneracy of the genetic code by splitting codon families into a hierarchy of robust and sensitive synonymous codons. Rates of protein synthesis associated with robust codons are up to 100-fold higher than those associated with sensitive codons under these conditions. We find that the observed hierarchy between synonymous codons is not determined by usual rules associated with tRNA abundance and codon usage. Rather, competition among tRNA isoacceptors for aminoacylation underlies the robustness of protein synthesis. Remarkably, the hierarchy established using the synthetic library also explains the measured robustness of synthesis for endogenous proteins in
E. coli
. We further found that the same hierarchy is reflected in the fitness cost of synonymous mutations in amino acid biosynthesis genes and in the transcriptional control of σ-factor genes. Our study suggests that organisms can exploit degeneracy lifting as a general strategy to adapt protein synthesis to their environment.
CD200-expressing human basal cell carcinoma cells initiate tumor growth
Authors: Colmont Chantal S. , BenKetah Antisar , Reed Simon H. , Hawk Nga V. , Telford William G. , Ohyama Manabu , Udey Mark C. , Yee Carole L. , Vogel Jonathan C. , Patel Girish K.
Published: January 2013

Smoothened antagonists directly target the genetic basis of human basal cell carcinoma (BCC), the most common of all cancers. These drugs inhibit BCC growth, but they are not curative. Although BCC cells are monomorphic, immunofluorescence microscopy reveals a complex hierarchical pattern of growth with inward differentiation along hair follicle lineages. Most BCC cells express the transcription factor KLF4 and are committed to terminal differentiation. A small CD200
+
CD45
−
BCC subpopulation that represents 1.63 ± 1.11% of all BCC cells resides in small clusters at the tumor periphery. By using reproducible in vivo xenograft growth assays, we determined that tumor initiating cell frequencies approximate one per 1.5 million unsorted BCC cells. The CD200
+
CD45
−
BCC subpopulation recreated BCC tumor growth in vivo with typical histological architecture and expression of sonic hedgehog-regulated genes. Reproducible in vivo BCC growth was achieved with as few as 10,000 CD200
+
CD45
−
cells, representing ∼1,500-fold enrichment. CD200
−
CD45
−
BCC cells were unable to form tumors. These findings establish a platform to study the effects of Smoothened antagonists on BCC tumor initiating cell and also suggest that currently available anti-CD200 therapy be considered, either as monotherapy or an adjunct to Smoothened antagonists, in the treatment of inoperable BCC.
Airway reopening through catastrophic events in a hierarchical network
Authors: Baudoin Michael , Song Yu , Manneville Paul , Baroud Charles N.
Published: January 2013

When you reach with your straw for the final drops of a milkshake, the liquid forms a train of plugs that flow slowly initially because of the high viscosity. They then suddenly rupture and are replaced with a rapid airflow with the characteristic slurping sound. Trains of liquid plugs also are observed in complex geometries, such as porous media during petroleum extraction, in microfluidic two-phase flows, or in flows in the pulmonary airway tree under pathological conditions. The dynamics of rupture events in these geometries play the dominant role in the spatial distribution of the flow and in determining how much of the medium remains occluded. Here we show that the flow of a train of plugs in a straight channel is always unstable to breaking through a cascade of ruptures. Collective effects considerably modify the rupture dynamics of plug trains: Interactions among nearest neighbors take place through the wetting films and slow down the cascade, whereas global interactions, through the total resistance to flow of the train, accelerate the dynamics after each plug rupture. In a branching tree of microchannels, similar cascades occur along paths that connect the input to a particular output. This divides the initial tree into several independent subnetworks, which then evolve independently of one another. The spatiotemporal distribution of the cascades is random, owing to strong sensitivity to the plug divisions at the bifurcations.
DnaA binding locus
datA
promotes DnaA-ATP hydrolysis to enable cell cycle-coordinated replication initiation
Authors: Kasho Kazutoshi , Katayama Tsutomu
Published: January 2013

The initiation of chromosomal DNA replication is rigidly regulated to ensure that it occurs in a cell cycle-coordinated manner. To ensure this in
Escherichia coli
, multiple systems regulate the activity of the replication initiator ATP-DnaA. The level of ATP-DnaA increases before initiation after which it drops via DnaA-ATP hydrolysis, yielding initiation-inactive ADP-DnaA. DnaA-ATP hydrolysis is crucial to regulation of initiation and mainly occurs by a replication-coupled feedback mechanism named RIDA (regulatory inactivation of DnaA). Here, we report a second DnaA-ATP hydrolysis system that occurs at the chromosomal site
datA
. This locus has been annotated as a reservoir for DnaA that binds many DnaA molecules in a manner dependent upon the nucleoid-associated factor IHF (integration host factor), resulting in repression of untimely initiations; however, there is no direct evidence for the binding of many DnaA molecules at this locus. We reveal that a complex consisting of
datA
and IHF promotes DnaA-ATP hydrolysis in a manner dependent on specific inter-DnaA interactions. Deletion of
datA
or the
ihf
gene increased ATP-DnaA levels to the maximal attainable levels in RIDA-defective cells. Cell-cycle analysis suggested that IHF binds to
datA
just after replication initiation at a time when RIDA is activated. We propose a model in which cell cycle-coordinated ATP-DnaA inactivation is regulated in a concerted manner by RIDA and
datA
.
Robust and tunable circadian rhythms from differentially sensitive catalytic domains
Authors: Phong Connie , Markson Joseph S. , Wilhoite Crystal M. , Rust Michael J.
Published: January 2013

Circadian clocks are ubiquitous biological oscillators that coordinate an organism’s behavior with the daily cycling of the external environment. To ensure synchronization with the environment, the period of the clock must be maintained near 24 h even as amplitude and phase are altered by input signaling. We show that, in a reconstituted circadian system from cyanobacteria, these conflicting requirements are satisfied by distinct functions for two domains of the central clock protein KaiC: the C-terminal autokinase domain integrates input signals through the ATP/ADP ratio, and the slow N-terminal ATPase acts as an input-independent timer. We find that phosphorylation in the C-terminal domain followed by an ATPase cycle in the N-terminal domain is required to form the inhibitory KaiB•KaiC complexes that drive the dynamics of the clock. We present a mathematical model in which this ATPase-mediated delay in negative feedback gives rise to a compensatory mechanism that allows a tunable phase and amplitude while ensuring a robust circadian period.
Structural basis for the specific recognition of dual receptors by the homopolymeric pH 6 antigen (Psa) fimbriae of
Yersinia pestis
Authors: Bao Rui , Nair Manoj K. M. , Tang Wai-kwan , Esser Lothar , Sadhukhan Annapurna , Holland Robin L. , Xia Di , Schifferli Dieter M.
Published: January 2013

The pH 6 antigen (Psa) of
Yersinia pestis
consists of fimbriae that bind to two receptors: β1-linked galactosyl residues in glycosphingolipids and the phosphocholine group in phospholipids. Despite the ubiquitous presence of either moiety on the surface of many mammalian cells,
Y. pestis
appears to prefer interacting with certain types of human cells, such as macrophages and alveolar epithelial cells of the lung. The molecular mechanism of this apparent selectivity is not clear. Site-directed mutagenesis of the consensus choline-binding motif in the sequence of PsaA, the subunit of the Psa fimbrial homopolymer, identified residues that abolish galactosylceramide binding, phosphatidylcholine binding, or both. The crystal structure of PsaA in complex with both galactose and phosphocholine reveals separate receptor binding sites that share a common structural motif, thus suggesting a potential interaction between the two sites. Mutagenesis of this shared structural motif identified Tyr126, which is part of the choline-binding consensus sequence but is found in direct contact with the galactose in the structure of PsaA, important for both receptor binding. Thus, this structure depicts a fimbrial subunit that forms a polymeric adhesin with a unique arrangement of dual receptor binding sites. These findings move the field forward by providing insights into unique types of multiple receptor–ligand interactions and should steer research into the synthesis of dual receptor inhibitor molecules to slow down the rapid progression of plague.
Mechanism of proton-coupled quinone reduction in Photosystem II
Authors: Saito Keisuke , Rutherford A. William , Ishikita Hiroshi
Published: January 2013

Photosystem II uses light to drive water oxidation and plastoquinone (PQ) reduction. PQ reduction involves two PQ cofactors, QAand QB, working in series. QAis a one-electron carrier, whereas QBundergoes sequential reduction and protonation to form QBH2. QBH2exchanges with PQ from the pool in the membrane. Based on the atomic coordinates of the Photosystem II crystal structure, we analyzed the proton transfer (PT) energetics adopting a quantum mechanical/molecular mechanical approach. The potential-energy profile suggests that the initial PT to QB•–occurs from the protonated, D1-His252 to QB•–via D1-Ser264. The second PT is likely to occur from D1-His215 to QBH−via an H-bond with an energy profile with a single well, resulting in the formation of QBH2and the D1-His215 anion. The pathway for reprotonation of D1-His215–may involve bicarbonate, D1-Tyr246 and water in the QBsite. Formate ligation to Fe2+did not significantly affect the protonation of reduced QB, suggesting that formate inhibits QBH2release rather than its formation. The presence of carbonate rather than bicarbonate seems unlikely because the calculations showed that this greatly perturbed the potential of the nonheme iron, stabilizing the Fe3+state in the presence of QB•–, a situation not encountered experimentally. H-bonding from D1-Tyr246 and D2-Tyr244 to the bicarbonate ligand of the nonheme iron contributes to the stability of the semiquinones. A detailed mechanistic model for QBreduction is presented.
Essential role of postsynaptic NMDA receptors in developmental refinement of excitatory synapses
Authors: Zhang Zhong-wei , Peterson Matthew , Liu Hong
Published: January 2013

Neurons in the brains of newborns are usually connected with many other neurons through weak synapses. This early pattern of connectivity is refined through pruning of many immature connections and strengthening of the remaining ones. NMDA receptors (NMDARs) are essential for the development of excitatory synapses, but their role in synaptic refinement is controversial. Although chronic application of blockers or global knockdown of NMDARs disrupts developmental refinement in many parts of the brain, the ubiquitous presence of NMDARs makes it difficult to dissociate direct effects from indirect ones. We addressed this question in the thalamus by using genetic mosaic deletion of NMDARs. We demonstrate that pruning and strengthening of immature synapses are blocked in neurons without NMDARs, but occur normally in neighboring neurons with NMDARs. Our data support a model in which activation of NMDARs in postsynaptic neurons initiates synaptic refinement.
House-to-house human movement drives dengue virus transmission
Authors: Stoddard Steven T. , Forshey Brett M. , Morrison Amy C. , Paz-Soldan Valerie A. , Vazquez-Prokopec Gonzalo M. , Astete Helvio , Reiner Robert C. , Vilcarromero Stalin , Elder John P. , Halsey Eric S. , Kochel Tadeusz J. , Kitron Uriel , Scott Thomas W.
Published: January 2013

Dengue is a mosquito-borne disease of growing global health importance. Prevention efforts focus on mosquito control, with limited success. New insights into the spatiotemporal drivers of dengue dynamics are needed to design improved disease-prevention strategies. Given the restricted range of movement of the primary mosquito vector,
Aedes aegypti
, local human movements may be an important driver of dengue virus (DENV) amplification and spread. Using contact-site cluster investigations in a case-control design, we demonstrate that, at an individual level, risk for human infection is defined by visits to places where contact with infected mosquitoes is likely, independent of distance from the home. Our data indicate that house-to-house human movements underlie spatial patterns of DENV incidence, causing marked heterogeneity in transmission rates. At a collective level, transmission appears to be shaped by social connections because routine movements among the same places, such as the homes of family and friends, are often similar for the infected individual and their contacts. Thus, routine, house-to-house human movements do play a key role in spread of this vector-borne pathogen at fine spatial scales. This finding has important implications for dengue prevention, challenging the appropriateness of current approaches to vector control. We argue that reexamination of existing paradigms regarding the spatiotemporal dynamics of DENV and other vector-borne pathogens, especially the importance of human movement, will lead to improvements in disease prevention.
Local auxin biosynthesis regulation by PLETHORA transcription factors controls phyllotaxis in
Arabidopsis
Authors: Pinon Violaine , Prasad Kalika , Grigg Stephen P. , Sanchez-Perez Gabino F. , Scheres Ben
Published: January 2013

Lateral organ distribution at the shoot apical meristem defines specific and robust phyllotaxis patterns that have intrigued biologists and mathematicians for centuries.
In silico
studies have revealed that this self-organizing process can be recapitulated by modeling the polar transport of the phytohormone auxin. Phyllotactic patterns change between species and developmental stages, but the processes behind these variations have remained unknown. Here we use regional complementation experiments to reveal that phyllotactic switches in
Arabidopsis
shoots can be mediated by PLETHORA-dependent control of local auxin biosynthesis.
Fluorescent dopamine tracer resolves individual dopaminergic synapses and their activity in the brain
Authors: Rodriguez Pamela C. , Pereira Daniela B. , Borgkvist Anders , Wong Minerva Y. , Barnard Candace , Sonders Mark S. , Zhang Hui , Sames Dalibor , Sulzer David
Published: January 2013

We recently introduced fluorescent false neurotransmitters (FFNs) as optical tracers that enable the visualization of neurotransmitter release at individual presynaptic terminals. Here, we describe a pH-responsive FFN probe, FFN102, which as a polar dopamine transporter substrate selectively labels dopamine cell bodies and dendrites in ventral midbrain and dopaminergic synaptic terminals in dorsal striatum. FFN102 exhibits greater fluorescence emission in neutral than acidic environments, and thus affords a means to optically measure evoked release of synaptic vesicle content into the extracellular space. Simultaneously, FFN102 allows the measurement of individual synaptic terminal activity by following fluorescence loss upon stimulation. Thus, FFN102 enables not only the identification of dopamine cells and their processes in brain tissue, but also the optical measurement of functional parameters including dopamine transporter activity and dopamine release at the level of individual synapses. As such, the development of FFN102 demonstrates that, by bringing together organic chemistry and neuroscience, molecular entities can be generated that match the endogenous transmitters in selectivity and distribution, allowing for the study of both the microanatomy and functional plasticity of the normal and diseased nervous system.
China’s language input system in the digital age affects children’s reading development
Authors: Tan Li Hai , Xu Min , Chang Chun Qi , Siok Wai Ting
Published: January 2013

Written Chinese as a logographic system was developed over 3,000 y ago. Historically, Chinese children have learned to read by learning to associate the visuo-graphic properties of Chinese characters with lexical meaning, typically through handwriting. In recent years, however, many Chinese children have learned to use electronic communication devices based on the pinyin input method, which associates phonemes and English letters with characters. When children use
pinyin
to key in letters, their spelling no longer depends on reproducing the visuo-graphic properties of characters that are indispensable to Chinese reading, and, thus, typing in pinyin may conflict with the traditional learning processes for written Chinese. We therefore tested character reading ability and pinyin use by primary school children in three Chinese cites: Beijing (
n
= 466), Guangzhou (
n
= 477), and Jining (
n
= 4,908). Children with severe reading difficulty are defined as those who were normal in nonverbal IQ but two grades (i.e., 2 y) behind in character-reading achievement. We found that the overall incidence rate of severe reading difficulty appears to be much higher than ever reported on Chinese reading. Crucially, we found that children’s reading scores were significantly negatively correlated with their use of the pinyin input method, suggesting that pinyin typing on e-devices hinders Chinese reading development. The Chinese language has survived the technological challenges of the digital era, but the benefits of communicating digitally may come with a cost in proficient learning of written Chinese.
Structural basis for the activation mechanism of the PlcR virulence regulator by the quorum-sensing signal peptide PapR
Authors: Grenha Rosa , Slamti Leyla , Nicaise Magali , Refes Yacine , Lereclus Didier , Nessler Sylvie
Published: January 2013

The quorum-sensing regulator PlcR is the master regulator of most known virulence factors in
Bacillus cereus
. It is a helix-turn-helix (HTH)-type transcription factor activated upon binding of its cognate signaling peptide PapR on a tetratricopeptide repeat-type regulatory domain. The structural and functional properties of PlcR have defined a new family of sensor regulators, called the RNPP family (for Rap, NprR, PrgX, and PlcR), in Gram-positive bacteria. To fully understand the activation mechanism of PlcR, we took a closer look at the conformation changes induced upon binding of PapR and of its target DNA, known as PlcR-box. For that purpose we have determined the structures of the apoform of PlcR (Apo PlcR) and of the ternary complex of PlcR with PapR and the PlcR-box from the
plcA
promoter. Comparison of the apoform of PlcR with the previously published structure of the PlcR–PapR binary complex shows how a small conformational change induced in the C-terminal region of the tetratricopeptide repeat (TPR) domain upon peptide binding propagates via the linker helix to the N-terminal HTH DNA-binding domain. Further comparison with the PlcR–PapR–DNA ternary complex shows how the activation of the PlcR dimer allows the linker helix to undergo a drastic conformational change and subsequent proper positioning of the HTH domains in the major groove of the two half sites of the pseudopalindromic PlcR-box. Together with random mutagenesis experiments and interaction measurements using peptides from distinct pherogroups, this structural analysis allows us to propose a molecular mechanism for this functional switch.
Reversion of the
Arabidopsis
UV-B photoreceptor UVR8 to the homodimeric ground state
Authors: Heijde Marc , Ulm Roman
Published: January 2013

Plants require the UV-B photoreceptor UV RESISTANCE LOCUS 8 (UVR8) for acclimation and survival in sunlight. Upon UV-B perception, UVR8 switches instantaneously from a homodimeric to monomeric configuration, which leads to interaction with the key signaling protein CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) and induction of UV-B–protective responses. Here, we show that UVR8 monomerization is reversible in vivo, restoring the homodimeric ground state. We also demonstrate that the UVR8-interacting proteins REPRESSOR OF UV-B PHOTOMORPHOGENESIS (RUP)1 and RUP2 mediate UVR8 redimerization independently of COP1. UVR8 redimerization consequently disrupts the UVR8–COP1 interaction, which halts signaling. Our results identify a key role of RUP1- and RUP2-mediated UVR8 redimerization in photoreceptor inactivation, a crucial process that regenerates reactivatable UVR8 homodimers.
Neuronal Nogo-A negatively regulates dendritic morphology and synaptic transmission in the cerebellum
Authors: Petrinovic Marija M. , Hourez Raphael , Aloy Elisabeth M. , Dewarrat Gregoire , Gall David , Weinmann Oliver , Gaudias Julien , Bachmann Lukas C. , Schiffmann Serge N. , Vogt Kaspar E. , Schwab Martin E.
Published: January 2013

Neuronal signal integration as well as synaptic transmission and plasticity highly depend on the morphology of dendrites and their spines. Nogo-A is a membrane protein enriched in the adult central nervous system (CNS) myelin, where it restricts the capacity of axons to grow and regenerate after injury. Nogo-A is also expressed by certain neurons, in particular during development, but its physiological function in this cell type is less well understood. We addressed this question in the cerebellum, where Nogo-A is transitorily highly expressed in the Purkinje cells (PCs) during early postnatal development. We used general genetic ablation (KO) as well as selective overexpression of Nogo-A in PCs to analyze its effect on dendritogenesis and on the formation of their main input synapses from parallel (PFs) and climbing fibers (CFs). PC dendritic trees were larger and more complex in Nogo-A KO mice and smaller than in wild-type in Nogo-A overexpressing PCs. Nogo-A KO resulted in premature soma-to-dendrite translocation of CFs and an enlargement of the CF territory in the molecular layer during development. Although spine density was not influenced by Nogo-A, the size of postsynaptic densities of PF–PC synapses was negatively correlated with the Nogo-A expression level. Electrophysiological studies revealed that Nogo-A negatively regulates the strength of synaptic transmission at the PF–PC synapse. Thus, Nogo-A appears as a negative regulator of PC input synapses, which orchestrates cerebellar connectivity through regulation of synapse morphology and the size of the PC dendritic tree.
Hydroxylamine as an intermediate in ammonia oxidation by globally abundant marine archaea
Authors: Vajrala Neeraja , Martens-Habbena Willm , Sayavedra-Soto Luis A. , Schauer Andrew , Bottomley Peter J. , Stahl David A. , Arp Daniel J.
Published: January 2013

The ammonia-oxidizing archaea have recently been recognized as a significant component of many microbial communities in the biosphere. Although the overall stoichiometry of archaeal chemoautotrophic growth via ammonia (NH
3
) oxidation to nitrite (NO
2
−
) is superficially similar to the ammonia-oxidizing bacteria, genome sequence analyses point to a completely unique biochemistry. The only genomic signature linking the bacterial and archaeal biochemistries of NH
3
oxidation is a highly divergent homolog of the ammonia monooxygenase (AMO). Although the presumptive product of the putative AMO is hydroxylamine (NH
2
OH), the absence of genes encoding a recognizable ammonia-oxidizing bacteria-like hydroxylamine oxidoreductase complex necessitates either a novel enzyme for the oxidation of NH
2
OH or an initial oxidation product other than NH
2
OH. We now show through combined physiological and stable isotope tracer analyses that NH
2
OH is both produced and consumed during the oxidation of NH
3
to NO
2
−
by
Nitrosopumilus maritimus
, that consumption is coupled to energy conversion, and that NH
2
OH is the most probable product of the archaeal AMO homolog. Thus, despite their deep phylogenetic divergence, initial oxidation of NH
3
by bacteria and archaea appears mechanistically similar. They however diverge biochemically at the point of oxidation of NH
2
OH, the archaea possibly catalyzing NH
2
OH oxidation using a novel enzyme complex.
Solubility-based genetic screen identifies RING finger protein 126 as an E3 ligase for activation-induced cytidine deaminase
Authors: Delker Rebecca K. , Zhou Yanjiao , Strikoudis Alexandros , Stebbins C. Erec , Papavasiliou F. Nina
Published: January 2013

Protein–protein interactions are typically identified by either biochemical purification coupled to mass spectrometry or genetic approaches exemplified by the yeast two-hybrid assay; however, neither assay works well for the identification of cofactors for poorly soluble proteins. Solubility of a poorly soluble protein is thought to increase upon cofactor binding, possibly by masking otherwise exposed hydrophobic domains. We have exploited this notion to develop a high-throughput genetic screen to identify interacting partners of an insoluble protein fused to chloramphenicol acetyltransferase by monitoring the survival of bacteria in the presence of a drug. In addition to presenting proof-of-principle experiments, we apply this screen to activation-induced cytidine deaminase (AID), a poorly soluble protein that is essential for antibody diversification. We identify a unique cofactor, RING finger protein 126 (RNF126), verify its interaction by traditional techniques, and show that it has functional consequences as RNF126 is able to ubiquitylate AID. Our results underpin the value of this screening technique and suggest a unique form of AID regulation involving RNF126 and ubiquitylation.
Community surveillance enhances
Pseudomonas aeruginosa
virulence during polymicrobial infection
Authors: Korgaonkar Aishwarya , Trivedi Urvish , Rumbaugh Kendra P. , Whiteley Marvin
Published: January 2013

Most infections result from colonization by more than one microbe. Within such polymicrobial infections, microbes often display synergistic interactions that result in increased disease severity. Although many clinical studies have documented the occurrence of synergy in polymicrobial infections, little is known about the underlying molecular mechanisms. A prominent pathogen in many polymicrobial infections is
Pseudomonas aeruginosa
, a Gram-negative bacterium that displays enhanced virulence during coculture with Gram-positive bacteria. In this study we discovered that during coinfection,
P. aeruginosa
uses peptidoglycan shed by Gram-positive bacteria as a cue to stimulate production of multiple extracellular factors that possess lytic activity against prokaryotic and eukaryotic cells. Consequently,
P. aeruginosa
displays enhanced virulence in a
Drosophila
model of infection when cocultured with Gram-positive bacteria. Inactivation of a gene (
PA0601
) required for peptidoglycan sensing mitigated this phenotype. Using
Drosophila
and murine models of infection, we also show that peptidoglycan sensing results in
P. aeruginosa
-mediated reduction in the Gram-positive flora in the infection site. Our data suggest that
P. aeruginosa
has evolved a mechanism to survey the microbial community and respond to Gram-positive produced peptidoglycan through production of antimicrobials and toxins that not only modify the composition of the community but also enhance host killing. Additionally, our results suggest that therapeutic strategies targeting Gram-positive bacteria might be a viable approach for reducing the severity of
P. aeruginosa
polymicrobial infections.
Physical activity and obesity mediate the association between childhood motor function and adolescents’ academic achievement
Authors: Kantomaa Marko T. , Stamatakis Emmanuel , Kankaanpää Anna , Kaakinen Marika , Rodriguez Alina , Taanila Anja , Ahonen Timo , Järvelin Marjo-Riitta , Tammelin Tuija
Published: January 2013

The global epidemic of obesity and physical inactivity may have detrimental implications for young people’s cognitive function and academic achievement. This prospective study investigated whether childhood motor function predicts later academic achievement via physical activity, fitness, and obesity. The study sample included 8,061 children from the Northern Finland Birth Cohort 1986, which contains data about parent-reported motor function at age 8 y and self-reported physical activity, predicted cardiorespiratory fitness (cycle ergometer test), obesity (body weight and height), and academic achievement (grades) at age 16 y. Structural equation models with unstandardized (B) and standardized (β) coefficients were used to test whether, and to what extent, physical activity, cardiorespiratory fitness, and obesity at age 16 mediated the association between childhood motor function and adolescents’ academic achievement. Physical activity was associated with a higher grade-point average, and obesity was associated with a lower grade-point average in adolescence. Furthermore, compromised motor function in childhood had a negative indirect effect on adolescents’ academic achievement via physical inactivity (B = –0.023, 95% confidence interval = –0.031, –0.015) and obesity (B = –0.025, 95% confidence interval = –0.039, –0.011), but not via cardiorespiratory fitness. These results suggest that physical activity and obesity may mediate the association between childhood motor function and adolescents’ academic achievement. Compromised motor function in childhood may represent an important factor driving the effects of obesity and physical inactivity on academic underachievement.
Long-range protein–water dynamics in hyperactive insect antifreeze proteins
Authors: Meister Konrad , Ebbinghaus Simon , Xu Yao , Duman John G. , DeVries Arthur , Gruebele Martin , Leitner David M. , Havenith Martina
Published: January 2013

Antifreeze proteins (AFPs) are specific proteins that are able to lower the freezing point of aqueous solutions relative to the melting point. Hyperactive AFPs, identified in insects, have an especially high ability to depress the freezing point by far exceeding the abilities of other AFPs. In previous studies, we postulated that the activity of AFPs can be attributed to two distinct molecular mechanisms: (
i
) short-range direct interaction of the protein surface with the growing ice face and (
ii
) long-range interaction by protein-induced water dynamics extending up to 20 Å from the protein surface. In the present paper, we combine terahertz spectroscopy and molecular simulations to prove that long-range protein–water interactions make essential contributions to the high antifreeze activity of insect AFPs from the beetle
Dendroides canadensis
. We also support our hypothesis by studying the effect of the addition of the osmolyte sodium citrate.
Involvement of distinct arrestin-1 elements in binding to different functional forms of rhodopsin
Authors: Zhuang Tiandi , Chen Qiuyan , Cho Min-Kyu , Vishnivetskiy Sergey A. , Iverson Tina M. , Gurevich Vsevolod V. , Sanders Charles R.
Published: January 2013

Solution NMR spectroscopy of labeled arrestin-1 was used to explore its interactions with dark-state phosphorylated rhodopsin (P-Rh), phosphorylated opsin (P-opsin), unphosphorylated light-activated rhodopsin (Rh*), and phosphorylated light-activated rhodopsin (P-Rh*). Distinct sets of arrestin-1 elements were seen to be engaged by Rh* and inactive P-Rh, which induced conformational changes that differed from those triggered by binding of P-Rh*. Although arrestin-1 affinity for Rh* was seen to be low (
K
D
> 150 μM), its affinity for P-Rh (K
D
∼80 μM) was comparable to the concentration of active monomeric arrestin-1 in the outer segment, suggesting that P-Rh generated by high-gain phosphorylation is occupied by arrestin-1 under physiological conditions and will not signal upon photo-activation. Arrestin-1 was seen to bind P-Rh* and P-opsin with fairly high affinity (
K
D
of ∼50 and 800 nM, respectively), implying that arrestin-1 dissociation is triggered only upon P-opsin regeneration with 11-
cis
-retinal, precluding noise generated by opsin activity. Based on their observed affinity for arrestin-1, P-opsin and inactive P-Rh very likely affect the physiological monomer-dimer-tetramer equilibrium of arrestin-1, and should therefore be taken into account when modeling photoreceptor function. The data also suggested that complex formation with either P-Rh* or P-opsin results in a global transition in the conformation of arrestin-1, possibly to a dynamic molten globule-like structure. We hypothesize that this transition contributes to the mechanism that triggers preferential interactions of several signaling proteins with receptor-activated arrestins.