bluuebunny/crossref_metadata_2025 huggingface dataset:
Decoding moral judgments from neural representations of intentions
Authors: Koster-Hale Jorie , Saxe Rebecca , Dungan James , Young Liane L.
Published: March 2013

Intentional harms are typically judged to be morally worse than accidental harms. Distinguishing between intentional harms and accidents depends on the capacity for mental state reasoning (i.e., reasoning about beliefs and intentions), which is supported by a group of brain regions including the right temporo-parietal junction (RTPJ). Prior research has found that interfering with activity in RTPJ can impair mental state reasoning for moral judgment and that high-functioning individuals with autism spectrum disorders make moral judgments based less on intent information than neurotypical participants. Three experiments, using multivoxel pattern analysis, find that (
i
) in neurotypical adults, the RTPJ shows reliable and distinct spatial patterns of responses across voxels for intentional vs. accidental harms, and (
ii
) individual differences in this neural pattern predict differences in participants’ moral judgments. These effects are specific to RTPJ. By contrast, (
iii
) this distinction was absent in adults with autism spectrum disorders. We conclude that multivoxel pattern analysis can detect features of mental state representations (e.g., intent), and that the corresponding neural patterns are behaviorally and clinically relevant.
Mammalian target of rapamycin complex 1 activation negatively regulates Polo-like kinase 2-mediated homeostatic compensation following neonatal seizures
Authors: Sun Hongyu , Kosaras Bela , Klein Peter M. , Jensen Frances E.
Published: March 2013

Homeostatic plasticity is characterized by compensatory changes in synaptic strength and intrinsic membrane properties in response to chronic changes in neuronal activity. Neonatal seizures are a naturally occurring source of neuronal overactivation and can lead to long-term epilepsy and cognitive deficits. Using a rodent model of hypoxia-induced neonatal seizures that results in a persistent increase in AMPA receptor (AMPAR) function in hippocampal CA1 pyramidal neurons, we aimed to determine whether there was any evidence of an opposing endogenous homeostatic antiepileptic response. Given that this model results in long-term epilepsy, we also examined mechanisms whereby this homeostasis fails. Whole-cell patch-clamp recordings from neurons in slices removed at intervals following seizure onset revealed an initial up-regulation of AMPAR function that was followed by a transient dynamic attenuation of this enhancement by 48–72 h, although AMPAR function was still increased compared with nonseizure control baseline. This secondary down-regulation of enhanced AMPAR function was coincident with a marked transient increase in expression and function of the Polo-like kinase 2 (PLK2), which has previously been implicated in homeostatic down-regulation of neuronal excitability in cell/slice culture models. The effects were transient and at 1 wk AMPAR function once again became up-regulated, simultaneous with a decrease in PLK2 expression and function. This negative regulation was mediated by subacute postseizure increases in mammalian target of rapamycin (mTOR). Application of the mTOR inhibitor rapamycin prevented post-hypoxic seizure impairment of homeostasis, suggesting that homeostatic plasticity mechanisms may be potentially modifiable therapeutic targets in epileptogenesis.
Portraying the unique contribution of the default mode network to internally driven mnemonic processes
Authors: Shapira-Lichter Irit , Oren Noga , Jacob Yael , Gruberger Michal , Hendler Talma
Published: March 2013

Numerous neuroimaging studies have implicated default mode network (DMN) involvement in both internally driven processes and memory. Nevertheless, it is unclear whether memory operations reflect a particular case of internally driven processing or alternatively involve the DMN in a distinct manner, possibly depending on memory type. This question is critical for refining neurocognitive memory theorem in the context of other endogenic processes and elucidating the functional significance of this key network. We used functional MRI to examine DMN activity and connectivity patterns while participants overtly generated words according to nonmnemonic (phonemic) or mnemonic (semantic or episodic) cues. Overall, mnemonic word fluency was found to elicit greater DMN activity and stronger within-network functional connectivity compared with nonmnemonic fluency. Furthermore, two levels of functional organization of memory retrieval were shown. First, across both mnemonic tasks, activity was greater mainly in the posterior cingulate cortex, implying selective contribution to generic aspects of memory beyond its general involvement in endogenous processes. Second, parts of the DMN showed distinct selectivity for each of the mnemonic conditions; greater recruitment of the anterior prefrontal cortex, retroesplenial cortex, and hippocampi and elevated connectivity between anterior and posterior medial DMN nodes characterized the semantic condition, whereas increased recruitment of posterior DMN components and elevated connectivity between them characterized the episodic condition. This finding emphasizes the involvement of DMN elements in discrete aspects of memory retrieval. Altogether, our results show a specific contribution of the DMN to memory processes, corresponding to the specific type of memory retrieval.
Microfluidic processor allows rapid HER2 immunohistochemistry of breast carcinomas and significantly reduces ambiguous (2+) read-outs
Authors: Ciftlik Ata Tuna , Lehr Hans-Anton , Gijs Martin A. M.
Published: March 2013

Biomarker analysis is playing an essential role in cancer diagnosis, prognosis, and prediction. Quantitative assessment of immunohistochemical biomarker expression on tumor tissues is of clinical relevance when deciding targeted treatments for cancer patients. Here, we report a microfluidic tissue processor that permits accurate quantification of the expression of biomarkers on tissue sections, enabled by the ultra-rapid and uniform fluidic exchange of the device. An important clinical biomarker for invasive breast cancer is human epidermal growth factor receptor 2 [(HER2), also known as neu], a transmembrane tyrosine kinase that connotes adverse prognostic information for the patients concerned and serves as a target for personalized treatment using the humanized antibody trastuzumab. Unfortunately, when using state-of-the-art methods, the intensity of an immunohistochemical signal is not proportional to the extent of biomarker expression, causing ambiguous outcomes. Using our device, we performed tests on 76 invasive breast carcinoma cases expressing various levels of HER2. We eliminated more than 90% of the ambiguous results (
n
= 27), correctly assigning cases to the amplification status as assessed by in situ hybridization controls, whereas the concordance for HER2-negative (
n
= 31) and -positive (
n
= 18) cases was 100%. Our results demonstrate the clinical potential of microfluidics for accurate biomarker expression analysis. We anticipate our technique will be a diagnostic tool that will provide better and more reliable data, onto which future treatment regimes can be based.
Water oxidation surface mechanisms replicated by a totally inorganic tetraruthenium–oxo molecular complex
Authors: Piccinin Simone , Sartorel Andrea , Aquilanti Giuliana , Goldoni Andrea , Bonchio Marcella , Fabris Stefano
Published: March 2013

Solar-to-fuel energy conversion relies on the invention of efficient catalysts enabling water oxidation through low-energy pathways. Our aerobic life is based on this strategy, mastered by the natural Photosystem II enzyme, using a tetranuclear Mn–oxo complex as oxygen evolving center. Within artificial devices, water can be oxidized efficiently on tailored metal-oxide surfaces such as RuO
2
. The quest for catalyst optimization in vitro is plagued by the elusive description of the active sites on bulk oxides. Although molecular mimics of the natural catalyst have been proposed, they generally suffer from oxidative degradation under multiturnover regime. Here we investigate a nano-sized Ru
4
–polyoxometalate standing as an efficient artificial catalyst featuring a totally inorganic molecular structure with enhanced stability. Experimental and computational evidence reported herein indicates that this is a unique molecular species mimicking oxygenic RuO
2
surfaces. Ru
4
–polyoxometalate bridges the gap between homogeneous and heterogeneous water oxidation catalysis, leading to a breakthrough system. Density functional theory calculations show that the catalytic efficiency stems from the optimal distribution of the free energy cost to form reaction intermediates, in analogy with metal-oxide catalysts, thus providing a unifying picture for the two realms of water oxidation catalysis. These correlations among the mechanism of reaction, thermodynamic efficiency, and local structure of the active sites provide the key guidelines for the rational design of superior molecular catalysts and composite materials designed with a bottom–up approach and atomic control.
Shale gas development impacts on surface water quality in Pennsylvania
Authors: Olmstead Sheila M. , Muehlenbachs Lucija A. , Shih Jhih-Shyang , Chu Ziyan , Krupnick Alan J.
Published: March 2013

Concern has been raised in the scientific literature about the environmental implications of extracting natural gas from deep shale formations, and published studies suggest that shale gas development may affect local groundwater quality. The potential for surface water quality degradation has been discussed in prior work, although no empirical analysis of this issue has been published. The potential for large-scale surface water quality degradation has affected regulatory approaches to shale gas development in some US states, despite the dearth of evidence. This paper conducts a large-scale examination of the extent to which shale gas development activities affect surface water quality. Focusing on the Marcellus Shale in Pennsylvania, we estimate the effect of shale gas wells and the release of treated shale gas waste by permitted treatment facilities on observed downstream concentrations of chloride (Cl
−
) and total suspended solids (TSS), controlling for other factors. Results suggest that (
i
) the treatment of shale gas waste by treatment plants in a watershed raises downstream Cl
−
concentrations but not TSS concentrations, and (
ii
) the presence of shale gas wells in a watershed raises downstream TSS concentrations but not Cl
−
concentrations. These results can inform future voluntary measures taken by shale gas operators and policy approaches taken by regulators to protect surface water quality as the scale of this economically important activity increases.
Impact of insufficient sleep on total daily energy expenditure, food intake, and weight gain
Authors: Markwald Rachel R. , Melanson Edward L. , Smith Mark R. , Higgins Janine , Perreault Leigh , Eckel Robert H. , Wright Kenneth P.
Published: March 2013

Insufficient sleep is associated with obesity, yet little is known about how repeated nights of insufficient sleep influence energy expenditure and balance. We studied 16 adults in a 14- to 15-d-long inpatient study and quantified effects of 5 d of insufficient sleep, equivalent to a work week, on energy expenditure and energy intake compared with adequate sleep. We found that insufficient sleep increased total daily energy expenditure by ∼5%; however, energy intake—especially at night after dinner—was in excess of energy needed to maintain energy balance. Insufficient sleep led to 0.82 ± 0.47 kg (±SD) weight gain despite changes in hunger and satiety hormones ghrelin and leptin, and peptide YY, which signaled excess energy stores. Insufficient sleep delayed circadian melatonin phase and also led to an earlier circadian phase of wake time. Sex differences showed women, not men, maintained weight during adequate sleep, whereas insufficient sleep reduced dietary restraint and led to weight gain in women. Our findings suggest that increased food intake during insufficient sleep is a physiological adaptation to provide energy needed to sustain additional wakefulness; yet when food is easily accessible, intake surpasses that needed. We also found that transitioning from an insufficient to adequate/recovery sleep schedule decreased energy intake, especially of fats and carbohydrates, and led to −0.03 ± 0.50 kg weight loss. These findings provide evidence that sleep plays a key role in energy metabolism. Importantly, they demonstrate physiological and behavioral mechanisms by which insufficient sleep may contribute to overweight and obesity.
Phase geometries of two-dimensional excitable waves govern self-organized morphodynamics of amoeboid cells
Authors: Taniguchi Daisuke , Ishihara Shuji , Oonuki Takehiko , Honda-Kitahara Mai , Kaneko Kunihiko , Sawai Satoshi
Published: March 2013

In both randomly movingDictyosteliumand mammalian cells, phosphatidylinositol (3,4,5)-trisphosphate and F-actin are known to propagate as waves at the membrane and act to push out the protruding edge. To date, however, the relationship between the wave geometry and the patterns of amoeboid shape change remains elusive. Here, by using phase map analysis, we show that morphology dynamics of randomly movingDictyostelium discoideumcells can be characterized by the number, topology, and position of spatial phase singularities, i.e., points that represent organizing centers of rotating waves. A single isolated singularity near the cellular edge induced a rotational protrusion, whereas a pair of singularities supported a symmetric extension. These singularities appeared by strong phase resetting due to de novo nucleation at the back of preexisting waves. Analysis of a theoretical model indicated excitability of the system that is governed by positive feedback from phosphatidylinositol (3,4,5)-trisphosphate to PI3-kinase activation, and we showed experimentally that this requires F-actin. Furthermore, by incorporating membrane deformation into the model, we demonstrated that geometries of competing waves explain most of the observed semiperiodic changes in amoeboid morphology.
AMPA receptor/TARP stoichiometry visualized by single-molecule subunit counting
Authors: Hastie Peter , Ulbrich Maximilian H. , Wang Hui-Li , Arant Ryan J. , Lau Anthony G. , Zhang Zhenjie , Isacoff Ehud Y. , Chen Lu
Published: March 2013

Members of the transmembrane AMPA receptor-regulatory protein (TARP) family modulate AMPA receptor (AMPA-R) trafficking and function. AMPA-Rs consist of four pore-forming subunits. Previous studies show that TARPs are an integral part of the AMPA-R complex, acting as accessory subunits for mature receptors in vivo. The TARP/AMPA-R stoichiometry was previously measured indirectly and found to be variable and dependent on TARP expression level, with at most four TARPs associated with each AMPA-R complex. Here, we use a single-molecule technique in live cells that selectively images proteins located in the plasma membrane to directly count the number of TARPs associated with each AMPA-R complex. Although individual GFP-tagged TARP subunits are observed as freely diffusing fluorescent spots on the surface of
Xenopus laevis
oocytes when expressed alone, coexpression with AMPA-R–mCherry immobilizes the stargazin-GFP spots at sites of AMPA-R–mCherry, consistent with complex formation. We determined the number of TARP molecules associated with each AMPA-R by counting bleaching steps for three different TARP family members: γ-2, γ-3, and γ-4. We confirm that the TARP/AMPA-R stoichiometry depends on TARP expression level and discover that the maximum number of TARPs per AMPA-R complex falls into two categories: up to four γ-2 or γ-3 subunits, but rarely above two for γ-4 subunit. This unexpected AMPA-R/TARP stoichiometry difference has important implications for the assembly and function of TARP/AMPA-R complexes.
Private traits and attributes are predictable from digital records of human behavior
Authors: Kosinski Michal , Stillwell David , Graepel Thore
Published: March 2013

We show that easily accessible digital records of behavior, Facebook Likes, can be used to automatically and accurately predict a range of highly sensitive personal attributes including: sexual orientation, ethnicity, religious and political views, personality traits, intelligence, happiness, use of addictive substances, parental separation, age, and gender. The analysis presented is based on a dataset of over 58,000 volunteers who provided their Facebook Likes, detailed demographic profiles, and the results of several psychometric tests. The proposed model uses dimensionality reduction for preprocessing the Likes data, which are then entered into logistic/linear regression to predict individual psychodemographic profiles from Likes. The model correctly discriminates between homosexual and heterosexual men in 88% of cases, African Americans and Caucasian Americans in 95% of cases, and between Democrat and Republican in 85% of cases. For the personality trait “Openness,” prediction accuracy is close to the test–retest accuracy of a standard personality test. We give examples of associations between attributes and Likes and discuss implications for online personalization and privacy.
The role of long-range connections on the specificity of the macaque interareal cortical network
Authors: Markov Nikola T. , Ercsey-Ravasz Maria , Lamy Camille , Ribeiro Gomes Ana Rita , Magrou Loïc , Misery Pierre , Giroud Pascale , Barone Pascal , Dehay Colette , Toroczkai Zoltán , Knoblauch Kenneth , Van Essen David C. , Kennedy Henry
Published: March 2013

We investigated the influence of interareal distance on connectivity patterns in a database obtained from the injection of retrograde tracers in 29 areas distributed over six regions (occipital, temporal, parietal, frontal, prefrontal, and limbic). One-third of the 1,615 pathways projecting to the 29 target areas were reported only recently and deemed new-found projections (NFPs). NFPs are predominantly long-range, low-weight connections. A minimum dominating set analysis (a graph theoretic measure) shows that NFPs play a major role in globalizing input to small groups of areas. Randomization tests show that (
i
) NFPs make important contributions to the specificity of the connectivity profile of individual cortical areas, and (
ii
) NFPs share key properties with known connections at the same distance. We developed a similarity index, which shows that intraregion similarity is high, whereas the interregion similarity declines with distance. For area pairs, there is a steep decline with distance in the similarity and probability of being connected. Nevertheless, the present findings reveal an unexpected binary specificity despite the high density (66%) of the cortical graph. This specificity is made possible because connections are largely concentrated over short distances. These findings emphasize the importance of long-distance connections in the connectivity profile of an area. We demonstrate that long-distance connections are particularly prevalent for prefrontal areas, where they may play a prominent role in large-scale communication and information integration.
TLR9 mediates cellular protection by modulating energy metabolism in cardiomyocytes and neurons
Authors: Shintani Yasunori , Kapoor Amar , Kaneko Masahiro , Smolenski Ryszard T. , D’Acquisto Fulvio , Coppen Steven R. , Harada-Shoji Narumi , Lee Hack Jae , Thiemermann Christoph , Takashima Seiji , Yashiro Kenta , Suzuki Ken
Published: March 2013

Toll-like receptors (TLRs) are the central players in innate immunity. In particular, TLR9 initiates inflammatory response by recognizing DNA, imported by infection or released from tissue damage. Inflammation is, however, harmful to terminally differentiated organs, such as the heart and brain, with poor regenerative capacity, yet the role of TLR9 in such nonimmune cells, including cardiomyocytes and neurons, is undefined. Here we uncover an unexpected role of TLR9 in energy metabolism and cellular protection in cardiomyocytes and neurons. TLR9 stimulation reduced energy substrates and increased the AMP/ATP ratio, subsequently activating AMP-activated kinase (AMPK), leading to increased stress tolerance against hypoxia in cardiomyocytes without inducing the canonical inflammatory response. Analysis of the expression profiles between cardiomyocytes and macrophages identified that unc93 homolog B1 (
C. elegans
) was a pivotal switch for the distinct TLR9 responses by regulating subcellular localization of TLR9. Furthermore, this alternative TLR9 signaling was also found to operate in differentiated neuronal cells. These data propose an intriguing model that the same ligand–receptor can concomitantly increase the stress tolerance in cardiomyocytes and neurons, whereas immune cells induce inflammation upon tissue injury.
Homologs of vertebrate Opn3 potentially serve as a light sensor in nonphotoreceptive tissue
Authors: Koyanagi Mitsumasa , Takada Eiichiro , Nagata Takashi , Tsukamoto Hisao , Terakita Akihisa
Published: March 2013

Most opsins selectively bind 11-
cis
retinal as a chromophore to form a photosensitive pigment, which underlies various physiological functions, such as vision and circadian photoentrainment. Recently, opsin 3 (Opn3), originally called encephalopsin or panopsin, and its homologs were identified in various tissues including brain, eye, and liver in both vertebrates and invertebrates, including human. Because Opn3s are mainly expressed in tissues that are not considered to contain sufficient amounts of 11-
cis
retinal to form pigments, the photopigment formation ability of Opn3 has been of interest. Here, we report the successful expression of Opn3 homologs, pufferfish teleost multiple tissue opsin (PufTMT) and mosquito Opn3 (MosOpn3) and show that these proteins formed functional photopigments with 11-
cis
and 9-
cis
retinals. The PufTMT- and MosOpn3-based pigments have absorption maxima in the blue-to-green region and exhibit a bistable nature. These Opn3 homolog-based pigments activate G
i
-type and G
o
-type G proteins light dependently, indicating that they potentially serve as light-sensitive G
i
/G
o
-coupled receptors. We also demonstrated that mammalian cultured cells transfected with the MosOpn3 or PufTMT became light sensitive without the addition of 11-
cis
retinal and the photosensitivity retained after the continuous light exposure, showing a reusable pigment formation with retinal endogenously contained in culture medium. Interestingly, we found that the MosOpn3 also acts as a light sensor when constituted with 13-
cis
retinal, a ubiquitously present retinal isomer. Our findings suggest that homologs of vertebrate Opn3 might function as photoreceptors in various tissues; furthermore, these Opn3s, particularly the mosquito homolog, could provide a promising optogenetic tool for regulating cAMP-related G protein-coupled receptor signalings.
Molecular mechanism of quinone signaling mediated through S-quinonization of a YodB family repressor QsrR
Authors: Ji Quanjiang , Zhang Liang , Jones Marcus B. , Sun Fei , Deng Xin , Liang Haihua , Cho Hoonsik , Brugarolas Pedro , Gao Yihe N. , Peterson Scott N. , Lan Lefu , Bae Taeok , He Chuan
Published: March 2013

Quinone molecules are intracellular electron-transport carriers, as well as critical intra- and extracellular signals. However, transcriptional regulation of quinone signaling and its molecular basis are poorly understood. Here, we identify a thiol-stress-sensing regulator YodB family transcriptional regulator as a central component of quinone stress response of
Staphylococcus aureus
, which we have termed the quinone-sensing and response repressor (QsrR). We also identify and confirm an unprecedented quinone-sensing mechanism based on the S-quinonization of the essential residue Cys-5. Structural characterizations of the QsrR–DNA and QsrR–menadione complexes further reveal that the covalent association of menadione directly leads to the release of QsrR from operator DNA following a 10° rigid-body rotation as well as a 9-Å elongation between the dimeric subunits. The molecular level characterization of this quinone-sensing transcriptional regulator provides critical insights into quinone-mediated gene regulation in human pathogens.
Library of synthetic transcriptional AND gates built with split T7 RNA polymerase mutants
Authors: Shis David L. , Bennett Matthew R.
Published: March 2013

The construction of synthetic gene circuits relies on our ability to engineer regulatory architectures that are orthogonal to the host’s native regulatory pathways. However, as synthetic gene circuits become larger and more complicated, we are limited by the small number of parts, especially transcription factors, that work well in the context of the circuit. The current repertoire of transcription factors consists of a limited selection of activators and repressors, making the implementation of transcriptional logic a complicated and component-intensive process. To address this, we modified bacteriophage T7 RNA polymerase (T7 RNAP) to create a library of transcriptional AND gates for use in
Escherichia coli
by first splitting the protein and then mutating the DNA recognition domain of the C-terminal fragment to alter its promoter specificity. We first demonstrate that split T7 RNAP is active in vivo and compare it with full-length enzyme. We then create a library of mutant split T7 RNAPs that have a range of activities when used in combination with a complimentary set of altered T7-specific promoters. Finally, we assay the two-input function of both wild-type and mutant split T7 RNAPs and find that regulated expression of the N- and C-terminal fragments of the split T7 RNAPs creates AND logic in each case. This work demonstrates that mutant split T7 RNAP can be used as a transcriptional AND gate and introduces a unique library of components for use in synthetic gene circuits.
Microscopic structure of water at elevated pressures and temperatures
Authors: Sahle Christoph J. , Sternemann Christian , Schmidt Christian , Lehtola Susi , Jahn Sandro , Simonelli Laura , Huotari Simo , Hakala Mikko , Pylkkänen Tuomas , Nyrow Alexander , Mende Kolja , Tolan Metin , Hämäläinen Keijo , Wilke Max
Published: March 2013

We report on the microscopic structure of water at sub- and supercritical conditions studied using X-ray Raman spectroscopy, ab initio molecular dynamics simulations, and density functional theory. Systematic changes in the X-ray Raman spectra with increasing pressure and temperature are observed. Throughout the studied thermodynamic range, the experimental spectra can be interpreted with a structural model obtained from the molecular dynamics simulations. A spatial statistical analysis using Ripley’s K-function shows that this model is homogeneous on the nanometer length scale. According to the simulations, distortions of the hydrogen-bond network increase dramatically when temperature and pressure increase to the supercritical regime. In particular, the average number of hydrogen bonds per molecule decreases to ≈0.6 at 600 °C andp= 134 MPa.
Optically triggering spatiotemporally confined GPCR activity in a cell and programming neurite initiation and extension
Authors: Karunarathne W. K. Ajith , Giri Lopamudra , Kalyanaraman Vani , Gautam N.
Published: March 2013

Significance

G-protein–coupled receptors control a variety of important cell behaviors. However, tools are not available to activate these receptors in selected areas of a cell and exert control over cell behavior. Here we recruit unique properties of nonrhodopsin opsins to activate all the major types of G-protein signaling in spatially confined regions of single cells. We show that this approach can be used to optically induce polarized cell behavior and refashion early neuron differentiation. This optical approach can be applied to control other cell behaviors such as immune cell migration and cardiomyocyte contraction.
ABCA1 dimer–monomer interconversion during HDL generation revealed by single-molecule imaging
Authors: Nagata Koh O. , Nakada Chieko , Kasai Rinshi S. , Kusumi Akihiro , Ueda Kazumitsu
Published: March 2013

The generation of high-density lipoprotein (HDL), one of the most critical events for preventing atherosclerosis, is mediated by ATP-binding cassette protein A1 (ABCA1). ABCA1 is known to transfer cellular cholesterol and phospholipids to apolipoprotein A-I (apoA-I) for generating discoidal HDL (dHDL) particles, composed of 100–200 lipid molecules surrounded by two apoA-I molecules; however, the regulatory mechanisms are still poorly understood. Here we observed ABCA1-GFP and apoA-I at the level of single molecules on the plasma membrane via a total internal reflection fluorescence microscope. We found that about 70% of total ABCA1-GFP spots are immobilized on the plasma membrane and estimated that about 89% of immobile ABCA1 molecules are in dimers. Furthermore, an ATPase-deficient ABCA1 mutant failed to be immobilized or form a dimer. We found that the lipid acceptor apoA-I interacts with the ABCA1 dimer to generate dHDL and is followed by ABCA1 dimer–monomer interconversion. This indicates that the formation of the ABCA1 dimer is the key for apoA-I binding and nascent HDL generation. Our findings suggest the physiological significance of conversion of the ABCA1 monomer to a dimer: The dimer serves as a receptor for two apoA-I molecules for dHDL particle generation.
Aluminum tolerance in maize is associated with higherMATE1gene copy number
Authors: Maron Lyza G. , Guimarães Claudia T. , Kirst Matias , Albert Patrice S. , Birchler James A. , Bradbury Peter J. , Buckler Edward S. , Coluccio Alison E. , Danilova Tatiana V. , Kudrna David , Magalhaes Jurandir V. , Piñeros Miguel A. , Schatz Michael C. , Wing Rod A. , Kochian Leon V.
Published: March 2013

Genome structure variation, including copy number variation and presence/absence variation, comprises a large extent of maize genetic diversity; however, its effect on phenotypes remains largely unexplored. Here, we describe how copy number variation underlies a rare allele that contributes to maize aluminum (Al) tolerance. Al toxicity is the primary limitation for crop production on acid soils, which make up 50% of the world’s potentially arable lands. In a recombinant inbred line mapping population, copy number variation of the Al tolerance gene multidrug and toxic compound extrusion 1 (MATE1) is the basis for the quantitative trait locus of largest effect on phenotypic variation. This expansion inMATE1copy number is associated with higherMATE1expression, which in turn results in superior Al tolerance. The threeMATE1copies are identical and are part of a tandem triplication. Only three maize inbred lines carrying the three-copy allele were identified from maize and teosinte diversity panels, indicating that copy number variation forMATE1is a rare, and quite likely recent, event. These maize lines with higherMATE1copy number are also Al-tolerant, have highMATE1expression, and originate from regions of highly acidic soils. Our findings show a role for copy number variation in the adaptation of maize to acidic soils in the tropics and suggest that genome structural changes may be a rapid evolutionary response to new environments.
Steroid-based facial amphiphiles for stabilization and crystallization of membrane proteins
Authors: Lee Sung Chang , Bennett Brad C. , Hong Wen-Xu , Fu Yu , Baker Kent A. , Marcoux Julien , Robinson Carol V. , Ward Andrew B. , Halpert James R. , Stevens Raymond C. , Stout Charles David , Yeager Mark J. , Zhang Qinghai
Published: March 2013

Significance

Membrane proteins (MPs) perform a variety of essential cellular functions, account for about one-third of encoded proteins in genomes, and comprise more than one-half of human drug targets. High-resolution structures are essential to understand the underlying molecular mechanisms of MPs and facilitate structure-based drug design efforts. Detergents are indispensible in the solubilization of MPs, but they tend to destabilize MPs and often impede the growth of well-ordered protein crystals. We describe a class of structurally unique detergents, designated as facial amphiphiles, which improved MP stability and success in the crystallization of different families of MPs.
Thiophene-based covalent organic frameworks
Authors: Bertrand Guillaume H. V. , Michaelis Vladimir K. , Ong Ta-Chung , Griffin Robert G. , Dincă Mircea
Published: March 2013

We report the synthesis and characterization of covalent organic frameworks (COFs) incorporating thiophene-based building blocks. We show that these are amenable to reticular synthesis, and that bent ditopic monomers, such as 2,5-thiophenediboronic acid, are defect-prone building blocks that are susceptible to synthetic variations during COF synthesis. The synthesis and characterization of an unusual charge transfer complex between thieno[3,2-
b
]thiophene-2,5-diboronic acid and tetracyanoquinodimethane enabled by the unique COF architecture is also presented. Together, these results delineate important synthetic advances toward the implementation of COFs in electronic devices.
Ring cycle for dilating and constricting the nuclear pore
Authors: Solmaz Sozanne R. , Blobel Günter , Melčák Ivo
Published: March 2013

We recently showed that the three “channel” nucleoporins, Nup54, Nup58, and Nup62, interact with each other through only four distinct sites and established the crystal structures of the two resulting “interactomes,” Nup54•Nup58 and Nup54•Nup62. We also reported instability of the Nup54•Nup58 interactome and previously determined the atomic structure of the relevant Nup58 segment by itself, demonstrating that it forms a twofold symmetric tetramer. Here, we report the crystal structure of the relevant free Nup54 segment and show that it forms a tetrameric, helical bundle that is structurally “conditioned” for instability by a central patch of polar hydrogen-bonded residues. Integrating these data with our previously reported results, we propose a “ring cycle” for dilating and constricting the nuclear pore. In essence, three homooligomeric rings, one consisting of eight modules of Nup58 tetramers, and two, each consisting of eight modules of Nup54 tetramers, are stacked in midplane and characterize a constricted pore of 10- to 20-nm diameter. In going to the dilated state, segments of one Nup58 and two Nup54 tetrameric modules reassort into a dodecameric module, eight of which form a single, heterooligomeric midplane ring, which is flexible in a diameter range of 40–50 nm. The ring cycle would be regulated by phenylalanine–glycine regions (“FG repeats”) of channel nups. Akin to ligand-gated channels, the dilated state of the midplane ring may be stabilized by binding of [cargo•transport-factor] complexes to FG repeats, thereby linking the ratio of constricted to dilated nuclear pores to cellular transport need.
Conformation-specific labeling of BamA and suppressor analysis suggest a cyclic mechanism for β-barrel assembly in
Escherichia coli
Authors: Rigel Nathan W. , Ricci Dante P. , Silhavy Thomas J.
Published: March 2013

In Gram-negative bacteria, integral outer membrane β-barrel proteins (OMPs) are assembled by the beta-barrel assembly machine (Bam) complex. The essential components of this complex are the OMP BamA [which contains a carboxyl-terminal β-barrel and an amino-terminal periplasmic module composed of five polypeptide transport associated (POTRA) domains] and the lipoprotein BamD. In
Escherichia coli
, the Bam complex also contains three nonessential lipoproteins (BamBCE), all of which require the barrel-proximal POTRA domain (P5) for stable interactions with BamA. We have previously reported that the BamA β-barrel assumes two different conformations. A method for conformation-specific labeling of BamA described here reveals that these conformers reflect the degree of surface exposure of the conserved sixth extracellular loop (L6). L6 is surface accessible in one conformation but not in the other, likely because it occupies the lumen of the BamA β-barrel in the latter case. A gain-of-function mutation that promotes Bam activity (
bamDR197L
) and a loss-of-function mutation that decreases the activity of Bam (Δ
bamE
) both favor surface exposure of BamA L6, suggesting that BamD and BamE normally act to control L6 exposure through opposing functions. These results, along with the synthetic lethality of the
bamDR197L
Δ
bamE
double mutant, imply a cyclic mechanism in which the Bam lipoproteins regulate the conformation of BamA during the OMP assembly reaction. Our results further suggest that BamDE controls L6 exposure via conformational signals transmitted through P5 to L6.
Differential expression profiles of glycosphingolipids in human breast cancer stem cells vs. cancer non-stem cells
Authors: Liang Yuh-Jin , Ding Yao , Levery Steven B. , Lobaton Marlin , Handa Kazuko , Hakomori Sen-itiroh
Published: March 2013

Previous studies demonstrated that certain glycosphingolipids (GSLs) are involved in various cell functions, such as cell growth and motility. Recent studies showed changes in GSL expression during differentiation of human embryonic stem cells; however, little is known about expression profiles of GSLs in cancer stem cells (CSCs). CSCs are a small subpopulation in cancer and are proposed as cancer-initiating cells, have been shown to be resistant to numerous chemotherapies, and may cause cancer recurrence. Here, we analyzed GSLs expressed in human breast CSCs by applying a CSC model induced through epithelial–mesenchymal transition, using mass spectrometry, TLC immunostaining, and cell staining. We found that (
i
) Fuc-(n)Lc4Cer and Gb3Cer were drastically reduced in CSCs, whereas GD2, GD3, GM2, and GD1a were greatly increased in CSCs; (
ii
) among various glycosyltransferases tested, mRNA levels for ST3GAL5, B4GALNT1, ST8SIA1, and ST3GAL2 were increased in CSCs, which could explain the increased expression of GD3, GD2, GM2, and GD1a in CSCs; (
iii
) the majority of GD2+ cells and GD3+ cells were detected in the CD44
hi
/CD24
lo
cell population; and (
iv
) knockdown of ST8SIA1 and B4GALNT1 significantly reduced the expression of GD2 and GD3 and caused a phenotype change from CSC to a non-CSC, which was detected by reduced mammosphere formation and cell motility. Our results provide insight into GSL profiles in human breast CSCs, indicate a functional role of GD2 and GD3 in CSCs, and suggest a possible novel approach in targeting human breast CSCs to interfere with cancer recurrence.
Pharmacokinetics and Tissue Distribution of Thiamphenicol and Florfenicol in Pacific White Shrimp Litopenaeus vannamei in Freshwater following Oral Administration
Authors: Fang Wenhong , Li Guolie , Zhou Shuai , Li Xincang , Hu Linlin , Zhou Junfang
Published: March 2013

This study evaluated the pharmacokinetic disposition of thiamphenicol (THA) and florfenicol (FLR) after oral administration of each at a single dose of 10 mg/kg body weight in Pacific white shrimp Litopenaeus vannamei held in freshwater at 25.0 ± 1.0°C. The THA and FLR concentrations in the hemolymph, muscle, and hepatopancreas were determined by HPLC. The profiles of hemolymph THA and FLR concentrations versus time were best described by a two-compartment open pharmacokinetic model with first-order absorption. The peak concentration (Cmax), peak time (Tmax), absorption half-life (t1/2ka) and elimination half-life (t1/2β) of THA in hemolymph were 7.96 μg/mL, 2 h, 0.666 h, and 10.659 h, respectively. The corresponding values for FLR were 5.53 μg/mL, 2 h, 1.069 h, and 17.360 h, respectively. After oral administration, THA and FLR were rapidly absorbed in white shrimp and THA in hemolymph was absorbed and eliminated more quickly than FLR. The parameters in muscle and hepatopancreas were calculated by a noncompartment model based on statistical moment theory. The Cmax, area under the concentration–time curve (AUC0-t), mean residue time (MRT0-t), and half-life (t1/2z) in muscle were 2.98 μg/g, 29.10 mg/kg·h, 9.77 h, and 6.84 h, respectively. The corresponding values for FLR were 1.91 μg/g, 15.97 mg/kg·h, 19.40 h, and 18.32 h, respectively. In muscle THA was eliminated more quickly than FLR. The peak concentrations of THA and FLR in the hepatopancreas were 204.25 and 164.22 μg/g, respectively, and the values for AUC0-t were 1,337.74 and 871.73 mg/kg·h, respectively, which were much higher than those in hemolymph and muscle. The in vitro protein-binding value of THA (28.38%) was lower than that of FLR (37.91%), which might be related to the finding that THA in Pacific white shrimp was absorbed and eliminated more quickly than FLR.

Received July 21, 2012; accepted November 23, 2012
Letter Transpositions within Morphemes and across Morpheme Boundaries
Authors: Beyersmann Elisabeth , McCormick Samantha F. , Rastle Kathleen
Published: March 2013

Recent evidence has revealed conflicting results regarding the influence of letter transpositions during the recognition of morphologically complex words. While some studies suggest that the disruption of the morpheme boundary through across-boundary transpositions (e.g., dar nk ess) leads to the absence of masked transposed-letter (TL) priming, other studies have found that TL priming occurs independently of whether or not letters have been transposed across the boundary. We conducted three experiments to test whether the difference between TL- within and TL-across priming is modulated by (a) the transposition of internal versus external letters of the stem (Experiment 1), (b) the overall proportion of affixed trials (Experiment 2), or (c) the relative frequency between prime and target (Experiment 3). The results revealed equal TL-within and TL-across boundary priming across all three experiments, which adds to previous findings suggesting that across-boundary transpositions do not interfere with the recognition of morphologically complex words.
CUL4B promotes replication licensing by up-regulating the CDK2–CDC6 cascade
Authors: Zou Yongxin , Mi Jun , Wang Wenxing , Lu Juanjuan , Zhao Wei , Liu Zhaojian , Hu Huili , Yang Yang , Gao Xiaoxing , Jiang Baichun , Shao Changshun , Gong Yaoqin
Published: March 2013

Cullin-RING ubiquitin ligases (CRLs) participate in the regulation of diverse cellular processes including cell cycle progression. Mutations in the X-linked CUL4B, a member of the cullin family, cause mental retardation and other developmental abnormalities in humans. Cells that are deficient in CUL4B are severely selected against in vivo in heterozygotes. Here we report a role of CUL4B in the regulation of replication licensing. Strikingly, CDC6, the licensing factor in replication, was positively regulated by CUL4B and contributed to the loading of MCM2 to chromatin. The positive regulation of CDC6 by CUL4B depends on CDK2, which phosphorylates CDC6, protecting it from APCCDH1-mediated degradation. Thus, aside being required for cell cycle reentry from quiescence, CDK2 also contributes to pre-replication complex assembly in G1 phase of cycling cells. Interestingly, the up-regulation of CDK2 by CUL4B is achieved via the repression of miR-372 and miR-373, which target CDK2. Our findings thus establish a CUL4B–CDK2–CDC6 cascade in the regulation of DNA replication licensing.
Oncogenes induce genotoxic stress by mitotic processing of unusual replication intermediates
Authors: Neelsen Kai J. , Zanini Isabella M.Y. , Herrador Raquel , Lopes Massimo
Published: March 2013

Oncogene-induced DNA replication stress activates the DNA damage response (DDR), a crucial anticancer barrier. DDR inactivation in these conditions promotes genome instability and tumor progression, but the underlying molecular mechanisms are elusive. We found that overexpression of both Cyclin E and Cdc25A rapidly slowed down replication forks and induced fork reversal, suggestive of increased topological stress. Surprisingly, these phenotypes, per se, are neither associated with chromosomal breakage nor with significant DDR activation. Oncogene-induced DNA breakage and DDR activation instead occurred upon persistent G2/M arrest or, in a checkpoint-defective context, upon premature CDK1 activation. Depletion of MUS81, a cell cycle–regulated nuclease, markedly limited chromosomal breakage and led to further accumulation of reversed forks. We propose that nucleolytic processing of unusual replication intermediates mediates oncogene-induced genotoxicity and that limiting such processing to mitosis is a central anti-tumorigenic function of the DNA damage checkpoints.
miR-612 suppresses the invasive-metastatic cascade in hepatocellular carcinoma
Authors: Tao Zhong-Hua , Wan Jin-Liang , Zeng Ling-Yao , Xie Lu , Sun Hui-Chuan , Qin Lun-Xiu , Wang Lu , Zhou Jian , Ren Zheng-Gang , Li Yi-Xue , Fan Jia , Wu Wei-Zhong
Published: March 2013

MicroRNAs (miRNAs) play a critical role in tumor metastasis. In this study, we identified a set of 32 miRNAs involved in hepatocellular carcinoma (HCC) metastasis. Among them, miR-612 was shown for the first time to have inhibitory effects on HCC proliferation, migration, invasion, and metastasis. AKT2 was verified to be one of the direct targets of miR-612, through which the epithelial–mesenchymal transition (EMT) and metastasis were inhibited. The level of miR-612 in HCC patients was inversely associated with tumor size, stage, EMT, and metastasis. Of particular importance, miR-612 is involved in both the initial and final steps of the metastatic cascade, by suppressing local invasion and distant colonization. The pleiotropic roles of miR-612 in the HCC metastatic cascade suggest that it could be an effective target for both early and advanced HCC.
Loop C and the mechanism of acetylcholine receptor–channel gating
Authors: Purohit Prasad , Auerbach Anthony
Published: March 2013

Agonist molecules at the two neuromuscular acetylcholine (ACh) receptor (AChR) transmitter-binding sites increase the probability of channel opening. In one hypothesis for AChR activation (“priming”), the capping of loop C at each binding site transfers energy independently to the distant gate over a discrete structural pathway. We used single-channel analyses to examine the experimental support for this proposal with regard to brief unliganded openings, the effects of loop-C modifications, the effects of mutations to residues either on or off the putative pathway, and state models for describing currents at low [ACh]. The results show that (a) diliganded and brief unliganded openings are generated by the same essential, global transition; (b) the radical manipulation of loop C does not prevent channel opening but impairs agonist binding; (c) both on- and off-pathway mutations alter gating by changing the relative stability of the open-channel conformation by local interactions rather than by perturbing a specific site–gate communication link; and (d) it is possible to estimate directly the rate constants for agonist dissociation from and association to both the low and high affinity forms of the AChR-binding site by using a cyclic kinetic model. We conclude that the mechanism of energy transfer between the binding sites and the gate remains an open question.
Homogeneous Einstein metrics on 𝐺₂/𝑇
Authors: Arvanitoyeorgos Andreas , Chrysikos Ioannis , Sakane Yusuke
Published: March 2013

We construct the Einstein equation for an invariant Riemannian metric on the exceptional full flag manifold

M
=

G
2

/

T

M=G_2/T

. By computing a Gröbner basis for a system of polynomials on six variables we prove that this manifold admits exactly two non-Kähler invariant Einstein metrics. Thus

G
2

/

T

G_2/T

turns out to be the first known example of an exceptional full flag manifold which admits a non-Kähler and not normal homogeneous Einstein metric.