bluuebunny/crossref_metadata_2025 huggingface dataset:
Release of content through mechano-sensitive gates in pressurized liposomes
Authors: Louhivuori Martti , Risselada H. Jelger , van der Giessen Erik , Marrink Siewert J.
Published: November 2010

Mechano-sensitive channels are ubiquitous membrane proteins that activate in response to increasing tension in the lipid membrane. They facilitate a sudden, nonselective release of solutes and water that safeguards the integrity of the cell in hypo- or hyper-osmotic shock conditions. We have simulated the rapid release of content from a pressurized liposome through a particular mechano-sensitive protein channel, MscL, embedded in the liposomal membrane. We show that a single channel is able to relax the liposome, stressed to the point of bursting, in a matter of microseconds. We map the full activation–deactivation cycle of MscL in near-atomic detail and are able to quantify the rapid decrease in liposomal stress as a result of channel activation. This provides a computational tool that opens the way to contribute to the rational design of functional nano-containers.
Violation of local realism with freedom of choice
Authors: Scheidl Thomas , Ursin Rupert , Kofler Johannes , Ramelow Sven , Ma Xiao-Song , Herbst Thomas , Ratschbacher Lothar , Fedrizzi Alessandro , Langford Nathan K. , Jennewein Thomas , Zeilinger Anton
Published: November 2010

Bell’s theorem shows that local realistic theories place strong restrictions on observable correlations between different systems, giving rise to Bell’s inequality which can be violated in experiments using entangled quantum states. Bell’s theorem is based on the assumptions of realism, locality, and the freedom to choose between measurement settings. In experimental tests, “loopholes” arise which allow observed violations to still be explained by local realistic theories. Violating Bell’s inequality while simultaneously closing all such loopholes is one of the most significant still open challenges in fundamental physics today. In this paper, we present an experiment that violates Bell’s inequality while simultaneously closing the locality loophole and addressing the freedom-of-choice loophole, also closing the latter within a reasonable set of assumptions. We also explain that the locality and freedom-of-choice loopholes can be closed only within nondeterminism, i.e., in the context of stochastic local realism.
Direct roles of the signaling kinase RSK2 in Cdc25C activation during
Xenopus
oocyte maturation
Authors: Wang Ruoning , Jung Sung Yun , Wu Chuan Fen , Qin Jun , Kobayashi Ryuji , Gallick Gary E. , Kuang Jian
Published: November 2010

The induction of M phase in eukaryotic cell cycles requires robust activation of Cdc2/cyclin B by Cdc25, which itself is robustly activated by serine/threonine phosphorylations. Although multiple protein kinases that directly activate Cdc25C have been identified, whether the combination of different primary phosphorylations of Cdc25C is sufficient to fully activate Cdc25C has not been determined. By analyzing the GST-Cdc25C phosphorylating activity in
Xenopus
egg extracts, we previously defined roles of MAPK and Cdc2/cyclin B in partially activating Cdc25C and predicted the presence of another major Cdc25C-activating kinase. In this study, we demonstrate that this missing kinase is RSK2, which phosphorylates three sites in Cdc25C and also partially activates Cdc25C. However, the phosphorylations catalyzed by MAPK, Cdc2, and RSK2 fail to fully activate Cdc25C, suggesting that additional biochemical events are required to fully activate this key cell cycle regulator.
Carbon isotope compositions of terrestrial C3 plants as indicators of (paleo)ecology and (paleo)climate
Authors: Kohn Matthew J.
Published: November 2010

A broad compilation of modern carbon isotope compositions in all C3 plant types shows a monotonic increase inδ13C with decreasing mean annual precipitation (MAP) that differs from previous models. Corrections for temperature, altitude, or latitude are smaller than previously estimated. As corrected for altitude, latitude, and theδ13C of atmospheric CO2, these data permit refined interpretation of MAP, paleodiet, and paleoecology of ecosystems dominated by C3 plants, either prior to 7–8 million years ago (Ma), or more recently at mid- to high latitudes. Twenty-nine published paleontological studies suggest preservational or scientific bias toward dry ecosystems, although wet ecosystems are also represented. Unambiguous isotopic evidence for C4 plants is lacking prior to 7–8 Ma, and hominid ecosystems at 4.4 Ma show no isotopic evidence for dense forests. Consideration of global plant biomass indicates that averageδ13C of C3 plants is commonly overestimated by approximately 2‰.
Prion disease susceptibility is affected by β-structure folding propensity and local side-chain interactions in PrP
Authors: Khan M. Qasim , Sweeting Braden , Mulligan Vikram Khipple , Arslan Pharhad Eli , Cashman Neil R. , Pai Emil F. , Chakrabartty Avijit
Published: November 2010

Prion diseases occur when the normally α-helical prion protein (PrP) converts to a pathological β-structured state with prion infectivity (PrP
Sc
). Exposure to PrP
Sc
from other mammals can catalyze this conversion. Evidence from experimental and accidental transmission of prions suggests that mammals vary in their prion disease susceptibility: Hamsters and mice show relatively high susceptibility, whereas rabbits, horses, and dogs show low susceptibility. Using a novel approach to quantify conformational states of PrP by circular dichroism (CD), we find that prion susceptibility tracks with the intrinsic propensity of mammalian PrP to convert from the native, α-helical state to a cytotoxic β-structured state, which exists in a monomer–octamer equilibrium. It has been controversial whether β-structured monomers exist at acidic pH; sedimentation equilibrium and dual-wavelength CD evidence is presented for an equilibrium between a β-structured monomer and octamer in some acidic pH conditions. Our X-ray crystallographic structure of rabbit PrP has identified a key helix-capping motif implicated in the low prion disease susceptibility of rabbits. Removal of this capping motif increases the β-structure folding propensity of rabbit PrP to match that of PrP from mouse, a species more susceptible to prion disease.
Neural repetition suppression to identity is abolished by other-race faces
Authors: Vizioli Luca , Rousselet Guillaume A. , Caldara Roberto
Published: November 2010

Human beings are remarkably skilled at recognizing faces, with the marked exception of other-race faces: the so-called “other-race effect.” As reported nearly a century ago [Feingold CA (1914)
Journal of Criminal Law and Police Science
5:39–51], this face-recognition impairment is accompanied by the popular belief that other-race faces all look alike. However, the neural mechanisms underlying this high-level “perceptual illusion” are still unknown. To address this question, we recorded high-resolution electrophysiological scalp signals from East Asian (EA) and Western Caucasian (WC) observers as they viewed two EA or WC faces. The first adaptor face was followed by a target face of either the same or different identity. We quantified repetition suppression (RS), a reduction in neural activity in stimulus-sensitive regions following stimulus repetition. Conventional electrophysiological analyses on target faces failed to reveal any RS effect. However, to fully account for the paired nature of RS events, we subtracted the signal elicited by target to adaptor faces for each single trial and performed unbiased spatiotemporal data-driven analyses. This unique approach revealed stronger RS to same-race faces of same identity in both groups of observers on the face-sensitive N170 component. Such neurophysiological modulation in RS suggests efficient identity coding for same-race faces. Strikingly, OR faces elicited identical RS regardless of identity, all looking alike to the neural population underlying the N170. Our data show that sensitivity to race begins early at the perceptual level, providing, after nearly 100 y of investigations, a neurophysiological correlate of the “all look alike” perceptual experience.
Recovering physical potentials from a model protein databank
Authors: Mullinax J. W. , Noid W. G.
Published: November 2010

Knowledge-based approaches frequently employ empirical relations to determine effective potentials for coarse-grained protein models directly from protein databank structures. Although these approaches have enjoyed considerable success and widespread popularity in computational protein science, their fundamental basis has been widely questioned. It is well established that conventional knowledge-based approaches do not correctly treat many-body correlations between amino acids. Moreover, the physical significance of potentials determined by using structural statistics from different proteins has remained obscure. In the present work, we address both of these concerns by introducing and demonstrating a theory for calculating transferable potentials directly from a databank of protein structures. This approach assumes that the databank structures correspond to representative configurations sampled from equilibrium solution ensembles for different proteins. Given this assumption, this physics-based theory exactly treats many-body structural correlations and directly determines the transferable potentials that provide a variationally optimized approximation to the free energy landscape for each protein. We illustrate this approach by first constructing a databank of protein structures using a model potential and then quantitatively recovering this potential from the structure databank. The proposed framework will clarify the assumptions and physical significance of knowledge-based potentials, allow for their systematic improvement, and provide new insight into many-body correlations and cooperativity in folded proteins.
Stochastic reaction-diffusion kinetics in the microscopic limit
Authors: Fange David , Berg Otto G. , Sjöberg Paul , Elf Johan
Published: November 2010

Quantitative analysis of biochemical networks often requires consideration of both spatial and stochastic aspects of chemical processes. Despite significant progress in the field, it is still computationally prohibitive to simulate systems involving many reactants or complex geometries using a microscopic framework that includes the finest length and time scales of diffusion-limited molecular interactions. For this reason, spatially or temporally discretized simulations schemes are commonly used when modeling intracellular reaction networks. The challenge in defining such coarse-grained models is to calculate the correct probabilities of reaction given the microscopic parameters and the uncertainty in the molecular positions introduced by the spatial or temporal discretization. In this paper we have solved this problem for the spatially discretized Reaction-Diffusion Master Equation; this enables a seamless and physically consistent transition from the microscopic to the macroscopic frameworks of reaction-diffusion kinetics. We exemplify the use of the methods by showing that a phosphorylation-dephosphorylation motif, commonly observed in eukaryotic signaling pathways, is predicted to display fluctuations that depend on the geometry of the system.
Spliced leader–based metatranscriptomic analyses lead to recognition of hidden genomic features in dinoflagellates
Authors: Lin Senjie , Zhang Huan , Zhuang Yunyun , Tran Bao , Gill John
Published: November 2010

Environmental transcriptomics (metatranscriptomics) for a specific lineage of eukaryotic microbes (e.g., Dinoflagellata) would be instrumental for unraveling the genetic mechanisms by which these microbes respond to the natural environment, but it has not been exploited because of technical difficulties. Using the recently discovered dinoflagellate mRNA-specific spliced leader as a selective primer, we constructed cDNA libraries (e-cDNAs) from one marine and two freshwater plankton assemblages. Small-scale sequencing of the e-cDNAs revealed functionally diverse transcriptomes proven to be of dinoflagellate origin. A set of dinoflagellate common genes and transcripts of dominant dinoflagellate species were identified. Further analyses of the dataset prompted us to delve into the existing, largely unannotated dinoflagellate EST datasets (DinoEST). Consequently, all four nucleosome core histones, two histone modification proteins, and a nucleosome assembly protein were detected, clearly indicating the presence of nucleosome-like machinery long thought not to exist in dinoflagellates. The isolation of rhodopsin from taxonomically and ecotypically diverse dinoflagellates and its structural similarity and phylogenetic affinity to xanthorhodopsin suggest a common genetic potential in dinoflagellates to use solar energy nonphotosynthetically. Furthermore, we found 55 cytoplasmic ribosomal proteins (RPs) from the e-cDNAs and 24 more from DinoEST, showing that the dinoflagellate phylum possesses all 79 eukaryotic RPs. Our results suggest that a sophisticated eukaryotic molecular machine operates in dinoflagellates that likely encodes many more unsuspected physiological capabilities and, meanwhile, demonstrate that unique spliced leaders are useful for profiling lineage-specific microbial transcriptomes in situ.
Dually inducible TetON systems for tissue-specific conditional gene expression in zebrafish
Authors: Knopf Franziska , Schnabel Kristin , Haase Christa , Pfeifer Katja , Anastassiadis Konstantinos , Weidinger Gilbert
Published: November 2010

Systems for spatial and temporal control of gene expression are essential for developmental studies and are of particular importance for research in adult model organisms. We present two modified dually inducible TetON systems for tissue-specific conditional control of gene expression in zebrafish based on (
i
) a tetracycline inducible transcriptional activator (TetActivator) fused to the ligand binding domain of a mutated glucocorticoid receptor (TetA-GBD) and (
ii
) a TetActivator fused with a domain of the Ecdysone receptor (TetA-EcR). Both systems showed strong induction of tetracycline-responsive promoters upon administration of the appropriate ligands (doxycycline and dexamethasone for TetA-GBD, and doxycycline and tebufenozide for TetA-EcR), and undetectable leakiness when compared with classical TetActivators. Combinations of transgenic lines expressing TetA-GBD specifically in the heart or the CNS with different Tet-responsive transgenic lines allows conditional and tissue-specific control of gene expression in embryos and adults. Importantly, induction is fully reversible and tunable by the doses of drugs used. The TetA-EcR system avoids the possible side effects of dexamethasone and displays improved sensitivity both in zebrafish and in mammalian cells. These results show that dually inducible TetON systems are convenient tools for reversible and very tightly controlled conditional gene expression in zebrafish.
Emergence of resting state networks in the preterm human brain
Authors: Doria Valentina , Beckmann Christian F. , Arichi Tomoki , Merchant Nazakat , Groppo Michela , Turkheimer Federico E. , Counsell Serena J. , Murgasova Maria , Aljabar Paul , Nunes Rita G. , Larkman David J. , Rees Geraint , Edwards A. David
Published: November 2010

The functions of the resting state networks (RSNs) revealed by functional MRI remain unclear, but it has seemed possible that networks emerge in parallel with the development of related cognitive functions. We tested the alternative hypothesis: that the full repertoire of resting state dynamics emerges during the period of rapid neural growth before the normal time of birth at term (around 40 wk of gestation). We used a series of independent analytical techniques to map in detail the development of different networks in 70 infants born between 29 and 43 wk of postmenstrual age (PMA). We characterized and charted the development of RSNs from recognizable but often fragmentary elements at 30 wk of PMA to full facsimiles of adult patterns at term. Visual, auditory, somatosensory, motor, default mode, frontoparietal, and executive control networks developed at different rates; however, by term, complete networks were present, several of which were integrated with thalamic activity. These results place the emergence of RSNs largely during the period of rapid neural growth in the third trimester of gestation, suggesting that they are formed before the acquisition of cognitive competencies in later childhood.
High brain lactate is a hallmark of aging and caused by a shift in the lactate dehydrogenase A/B ratio
Authors: Ross Jaime M. , Öberg Johanna , Brené Stefan , Coppotelli Giuseppe , Terzioglu Mügen , Pernold Karin , Goiny Michel , Sitnikov Rouslan , Kehr Jan , Trifunovic Aleksandra , Larsson Nils-Göran , Hoffer Barry J. , Olson Lars
Published: November 2010

At present, there are few means to track symptomatic stages of CNS aging. Thus, although metabolic changes are implicated in mtDNA mutation-driven aging, the manifestations remain unclear. Here, we used normally aging and prematurely aging mtDNA mutator mice to establish a molecular link between mitochondrial dysfunction and abnormal metabolism in the aging process. Using proton magnetic resonance spectroscopy and HPLC, we found that brain lactate levels were increased twofold in both normally and prematurely aging mice during aging. To correlate the striking increase in lactate with tissue pathology, we investigated the respiratory chain enzymes and detected mitochondrial failure in key brain areas from both normally and prematurely aging mice. We used in situ hybridization to show that increased brain lactate levels were caused by a shift in transcriptional activities of the lactate dehydrogenases to promote pyruvate to lactate conversion. Separation of the five tetrameric lactate dehydrogenase (LDH) isoenzymes revealed an increase of those dominated by the
Ldh-A
product and a decrease of those rich in the
Ldh-B
product, which, in turn, increases pyruvate to lactate conversion. Spectrophotometric assays measuring LDH activity from the pyruvate and lactate sides of the reaction showed a higher pyruvate → lactate activity in the brain. We argue for the use of lactate proton magnetic resonance spectroscopy as a noninvasive strategy for monitoring this hallmark of the aging process. The mtDNA mutator mouse allows us to conclude that the increased LDH-A/LDH-B ratio causes high brain lactate levels, which, in turn, are predictive of aging phenotypes.
Observed suppression of ozone formation at extremely high temperatures due to chemical and biophysical feedbacks
Authors: Steiner Allison L. , Davis Adam J. , Sillman Sanford , Owen Robert C. , Michalak Anna M. , Fiore Arlene M.
Published: November 2010

Ground level ozone concentrations ([O
3
]) typically show a direct linear relationship with surface air temperature. Three decades of California measurements provide evidence of a statistically significant change in the ozone-temperature slope (Δ
m

O3-
T

) under extremely high temperatures (> 312 K). This Δ
m

O3-
T

leads to a plateau or decrease in [O
3
], reflecting the diminished role of nitrogen oxide sequestration by peroxyacetyl nitrates and reduced biogenic isoprene emissions at high temperatures. Despite inclusion of these processes in global and regional chemistry-climate models, a statistically significant change in Δ
m

O3-
T

has not been noted in prior studies. Future climate projections suggest a more frequent and spatially widespread occurrence of this Δ
m

O3-
T

response, confounding predictions of extreme ozone events based on the historically observed linear relationship.
Lissencephaly-1
controls germline stem cell self-renewal through modulating bone morphogenetic protein signaling and niche adhesion
Authors: Chen Shuyi , Kaneko Satoshi , Ma Xing , Chen Xiaochu , Ip Y. Tony , Xu Lan , Xie Ting
Published: November 2010

In the
Drosophila
ovary, bone morphogenetic protein (BMP) signaling activated by the niche promotes germline stem cell (GSC) self-renewal and proliferation, whereas E-cadherin–mediated cell adhesion anchors GSCs in the niche for their continuous self-renewal. Here we show that
Lissencephaly-1
(
Lis1
) regulates BMP signaling and E-cadherin–mediated adhesion between GSCs and their niche and thereby controls GSC self-renewal.
Lis1
mutant GSCs are lost faster than control GSCs because of differentiation but not because of cell death, indicating that
Lis1
controls GSC self-renewal. The
Lis1
mutant GSCs exhibit reduced BMP signaling activity, and
Lis1
interacts genetically with the BMP pathway components in the regulation of GSC maintenance. Mechanistically, Lis1 binds directly to and stabilizes the SMAD protein Mothers against decapentaplegic (Mad), facilitates its phosphorylation, and thereby regulates BMP signaling. Finally, the
Lis1
mutant GSCs accumulate less E-cadherin in the stem cell–niche junction than do their wild-type counterparts. Germline-specific expression of an activated BMP receptor thickveins (Tkv) or E-cadherin can partially rescue the loss phenotype of
Lis1
mutant GSCs. Therefore, this study has revealed a role of
Lis1
in the control of
Drosophila
ovarian GSC self-renewal, at least partly by regulating niche signal transduction and niche adhesion. It has been known that
Lis1
controls neural precursor/stem cell proliferation in the developing mammalian brain; this study further suggests that
Lis1
, which is widely expressed in adult mammalian tissues, could regulate adult tissue stem cells through modulating niche signaling and adhesion.
Phosphorylation of the spindle checkpoint protein Mad2 regulates its conformational transition
Authors: Kim Soonjoung , Sun Hongbin , Ball Haydn L. , Wassmann Katja , Luo Xuelian , Yu Hongtao
Published: November 2010

Regulated conformational changes of proteins are critical for cellular signal transduction. The spindle checkpoint protein Mad2 is an unusual protein with two native folds: the latent open conformer (O-Mad2) and the activated closed conformer (C-Mad2). During mitosis, cytosolic O-Mad2 binds to the Mad1–Mad2 core complex at unattached kinetochores and undergoes conformational activation to become C-Mad2. C-Mad2 binds to and inhibits Cdc20, an activator of APC/C, to prevent precocious anaphase onset. Here, we show that the conformational transition of Mad2 is regulated by phosphorylation of S195 in its C-terminal region. The phospho-mimicking Mad2
S195D
mutant and the phospho-S195 Mad2 protein obtained using intein-mediated semisynthesis do not form C-Mad2 on their own. Mad2
S195D
fails to bind to Cdc20, a low-affinity ligand, but still binds to high-affinity ligands, such as Mad1 and MBP1, forming ligand-bound C-Mad2. Overexpression of Mad2
S195D
in human cells causes checkpoint defects. Our results indicate that Mad2 phosphorylation inhibits its function through differentially regulating its binding to Mad1 and Cdc20 and establish that the conformational change of Mad2 is regulated by posttranslational mechanisms.
Pore opening and closing of a pentameric ligand-gated ion channel
Authors: Zhu Fangqiang , Hummer Gerhard
Published: November 2010

Nerve signaling in humans and chemical sensing in bacteria both rely on the controlled opening and closing of the ion-conducting pore in pentameric ligand-gated ion channels. With the help of a multiscale simulation approach that combines mixed elastic network model calculations with molecular dynamics simulations, we study the opening and closing of the pore in
Gloeobacter violaceus
channel GLIC at atomic resolution. In our simulations of the GLIC transmembrane domain, we first verify that the two endpoints of the transition are open and closed to sodium ion conduction, respectively. We then show that a two-stage tilting of the pore-lining helices induces cooperative drying and iris-like closing of the channel pore. From the free energy profile of the gating transition and from unrestrained simulations, we conclude that the pore of the isolated GLIC transmembrane domain closes spontaneously. The mechanical work of opening the pore is performed primarily on the M2-M3 loop. Strong interactions of this short and conserved loop with the extracellular domain are therefore crucial to couple ligand binding to channel opening.
Highly conserved tyrosine stabilizes the active state of rhodopsin
Authors: Goncalves Joseph A. , South Kieron , Ahuja Shivani , Zaitseva Ekaterina , Opefi Chikwado A. , Eilers Markus , Vogel Reiner , Reeves Philip J. , Smith Steven O.
Published: November 2010

Light-induced isomerization of the 11-
cis-
retinal chromophore in the visual pigment rhodopsin triggers displacement of the second extracellular loop (EL2) and motion of transmembrane helices H5, H6, and H7 leading to the active intermediate metarhodopsin II (Meta II). We describe solid-state NMR measurements of rhodopsin and Meta II that target the molecular contacts in the region of the ionic lock involving these three helices. We show that a contact between Arg135
3.50
and Met257
6.40
forms in Meta II, consistent with the outward rotation of H6 and breaking of the dark-state Glu134
3.49
-Arg135
3.50
-Glu247
6.30
ionic lock. We also show that Tyr223
5.58
and Tyr306
7.53
form molecular contacts with Met257
6.40
. Together these results reveal that the crystal structure of opsin in the region of the ionic lock reflects the active state of the receptor. We further demonstrate that Tyr223
5.58
and Ala132
3.47
in Meta II stabilize helix H5 in an active orientation. Mutation of Tyr223
5.58
to phenylalanine or mutation of Ala132
3.47
to leucine decreases the lifetime of the Meta II intermediate. Furthermore, the Y223F mutation is coupled to structural changes in EL2. In contrast, mutation of Tyr306
7.53
to phenylalanine shows only a moderate influence on the Meta II lifetime and is not coupled to EL2.
Commensal bacteria play a role in mating preference of
Drosophila melanogaster
Authors: Sharon Gil , Segal Daniel , Ringo John M. , Hefetz Abraham , Zilber-Rosenberg Ilana , Rosenberg Eugene
Published: November 2010

Development of mating preference is considered to be an early event in speciation. In this study, mating preference was achieved by dividing a population of
Drosophila melanogaster
and rearing one part on a molasses medium and the other on a starch medium. When the isolated populations were mixed, “molasses flies” preferred to mate with other molasses flies and “starch flies” preferred to mate with other starch flies. The mating preference appeared after only one generation and was maintained for at least 37 generations. Antibiotic treatment abolished mating preference, suggesting that the fly microbiota was responsible for the phenomenon. This was confirmed by infection experiments with microbiota obtained from the fly media (before antibiotic treatment) as well as with a mixed culture of
Lactobacillus
species and a pure culture of
Lactobacillus plantarum
isolated from starch flies. Analytical data suggest that symbiotic bacteria can influence mating preference by changing the levels of cuticular hydrocarbon sex pheromones. The results are discussed within the framework of the hologenome theory of evolution.
Single-electron pulses for ultrafast diffraction
Authors: Aidelsburger M. , Kirchner F. O. , Krausz F. , Baum P.
Published: November 2010

Visualization of atomic-scale structural motion by ultrafast electron diffraction and microscopy requires electron packets of shortest duration and highest coherence. We report on the generation and application of single-electron pulses for this purpose. Photoelectric emission from metal surfaces is studied with tunable ultraviolet pulses in the femtosecond regime. The bandwidth, efficiency, coherence, and electron pulse duration are investigated in dependence on excitation wavelength, intensity, and laser bandwidth. At photon energies close to the cathode’s work function, the electron pulse duration shortens significantly and approaches a threshold that is determined by interplay of the optical pulse width and the acceleration field. An optimized choice of laser wavelength and bandwidth results in sub-100-fs electron pulses. We demonstrate single-electron diffraction from polycrystalline diamond films and reveal the favorable influences of matched photon energies on the coherence volume of single-electron wave packets. We discuss the consequences of our findings for the physics of the photoelectric effect and for applications of single-electron pulses in ultrafast 4D imaging of structural dynamics.
RETRACTED: Testis-specific protein on Y chromosome (
TSPY
) represses the activity of the androgen receptor in androgen-dependent testicular germ-cell tumors
Authors: Akimoto Chihiro , Ueda Takashi , Inoue Kazuki , Yamaoka Ikuko , Sakari Matomo , Obara Wataru , Fujioka Tomoaki , Nagahara Akira , Nonomura Norio , Tsutsumi Syuichi , Aburatani Hiroyuki , Miki Tsuneharu , Matsumoto Takahiro , Kitagawa Hirochika , Kato Shigeaki
Published: November 2010

Testis-specific protein on Y chromosome (
TSPY
)
is an ampliconic gene on the Y chromosome, and genetic interaction with gonadoblastoma has been clinically established. However, the function of the TSPY protein remains to be characterized in physiological and pathological settings. In the present study, we observed coexpression of TSPY and the androgen receptor (AR) in testicular germ-cell tumors (TGCTs) in patients as well as in model cell lines, but such coexpression was not seen in normal testis of humans or mice. TSPY was a repressor for androgen signaling because of its trapping of cytosolic AR even in the presence of androgen. Androgen treatment stimulated cell proliferation of a TGCT model cell line, and TSPY potently attenuated androgen-dependent cell growth. Together with the finding that
TSPY
expression is reduced in more malignant TGCTs in vivo, the present study suggests that
TSPY
serves as a repressor in androgen-induced tumor development in TGCTs and raises the possibility that TSPY could be used as a clinical marker to assess the malignancy of TGCTs.
Chemoprevention by nonsteroidal anti-inflammatory drugs eliminates oncogenic intestinal stem cells via SMAC-dependent apoptosis
Authors: Qiu Wei , Wang Xinwei , Leibowitz Brian , Liu Hongtao , Barker Nick , Okada Hitoshi , Oue Naohide , Yasui Wataru , Clevers Hans , Schoen Robert E. , Yu Jian , Zhang Lin
Published: November 2010

Nonsteroidal anti-inflammatory drugs (NSAIDs) such as sulindac effectively prevent colon cancer in humans and rodent models. However, their cellular targets and underlying mechanisms have remained elusive. We found that dietary sulindac induced apoptosis to remove the intestinal stem cells with nuclear or phosphorylated β-catenin in
APC
Min/+
mice. NSAIDs also induced apoptosis in human colonic polyps and effectively removed cells with aberrant Wnt signaling. Furthermore, deficiency in SMAC, a mitochondrial apoptogenic protein, attenuated the tumor-suppressive effect of sulindac in
APC
Min/+
mice by blocking apoptosis and removal of stem cells with nuclear or phosphorylated β-catenin. These results suggest that effective chemoprevention of colon cancer by NSAIDs lies in the elimination of stem cells that are inappropriately activated by oncogenic events through induction of apoptosis.
Topographic maps of multisensory attention
Authors: Anderson Jeffrey S. , Ferguson Michael A. , Lopez-Larson Melissa , Yurgelun-Todd Deborah
Published: November 2010

The intraparietal sulcus (IPS) region is uniquely situated at the intersection of visual, somatosensory, and auditory association cortices, ideally located for processing of multisensory attention. We examined the internal architecture of the IPS region and its connectivity to other regions in the dorsal attention and cinguloinsular networks using maximal connectivity clustering. We show with resting state fMRI data from 58 healthy adolescent and young adult volunteers that points of maximal connectivity between the IPS and other regions in the dorsal attention and cinguloinsular networks are topographically organized, with at least seven maps of the IPS region in each hemisphere. Distinct clusters of the IPS exhibited differential connectivity to auditory, visual, somatosensory, and default mode networks, suggesting local specialization within the IPS region for different sensory modalities. In an independent task activation paradigm with 16 subjects, attention to different sensory modalities showed similar functional specialization within the left intraparietal sulcus region. The default mode network, in contrast, did not show a topographical relationship between regions in the network, but rather maximal connectivity in each region to a single central cluster of the other regions. The topographical architecture of multisensory attention may represent a mechanism for specificity in top-down control of attention from dorsolateral prefrontal and lateral orbitofrontal cortex and may represent an organizational unit for multisensory representations in the brain.
Massively parallel sequencing for monitoring genetic consistency and quality control of live viral vaccines
Authors: Neverov Alexander , Chumakov Konstantin
Published: November 2010

Intrinsic genetic instability of RNA viruses may lead to the accumulation of revertants during manufacture of live viral vaccines, requiring rigorous quality control to ensure vaccine safety. Each lot of oral poliovirus vaccine (OPV) is tested for neurovirulence in animals and also for the presence of neurovirulent revertants. Mutant analysis by PCR and restriction enzyme cleavage (MAPREC) is used to measure the frequency of neurovirulent mutations at the 5′ untranslated region (UTR) of the viral genome that correlate with the level of neurovirulence determined by the monkey neurovirulence test. However, MAPREC can only monitor mutations at a few genomic loci and miss mutations at other sites that could adversely affect vaccine quality. Here we propose to use massively parallel sequencing (MPS) for sensitive detection and quantification of all mutations in the entire genome of attenuated viruses. Analysis of vaccine samples and reference preparations demonstrated a perfect agreement with MAPREC results. Quantitative MPS analysis of validated reference preparations tested by MAPREC produced identical results, suggesting that the method could take advantage of the existing reference materials and be used as a replacement for the MAPREC procedure in lot release of OPV. Patterns of mutations present at a low level in vaccine preparations were characteristic of seed viruses used for their manufacture and could be used for identification of individual batches. This approach may represent the ultimate tool for monitoring genetic consistency of live viral vaccines.
Radiometric dating of the type-site forHomo heidelbergensisat Mauer, Germany
Authors: Wagner Günther A. , Krbetschek Matthias , Degering Detlev , Bahain Jean-Jacques , Shao Qingfeng , Falguères Christophe , Voinchet Pierre , Dolo Jean-Michel , Garcia Tristan , Rightmire G. Philip
Published: November 2010

The Mauer mandible, holotype ofHomo heidelbergensis, was found in 1907 in fluvial sands deposited by the Neckar River 10 km southeast of Heidelberg, Germany. The fossil is an important key to understanding early human occupation of Europe north of the Alps. Given the associated mammal fauna and the geological context, the find layer has been placed in the early Middle Pleistocene, but confirmatory chronometric evidence has hitherto been missing. Here we show that two independent techniques, the combined electron spin resonance/U-series method used with mammal teeth and infrared radiofluorescence applied to sand grains, date the type-site ofHomo heidelbergensisat Mauer to 609 ± 40 ka. This result demonstrates that the mandible is the oldest hominin fossil reported to date from central and northern Europe and raises questions concerning the phyletic relationship ofHomo heidelbergensisto more ancient populations documented from southern Europe and in Africa. We address the paleoanthropological significance of the Mauer jaw in light of this dating evidence.
Differential correction of lagging-strand replication errors made by DNA polymerases α and δ
Authors: Nick McElhinny Stephanie A. , Kissling Grace E. , Kunkel Thomas A.
Published: November 2010

Mismatch repair (MMR) of replication errors requires DNA ends that can direct repair to the newly synthesized strand containing the error. For all but those organisms that use adenine methylation to generate nicks, the source of these ends in vivo is unknown. One possibility is that MMR may have a “special relation to the replication complex” [Wagner R, Jr., Meselson M (1976)
Proc Natl Acad Sci USA
73:4135–4139], perhaps one that allows 5′ or 3′ DNA ends associated with replication to act as strand discrimination signals. Here we examine this hypothesis, based on the logic that errors made by yeast DNA polymerase α (Pol α), which initiates Okazaki fragments during lagging-strand replication, will always be closer to a 5′ end than will be more internal errors generated by DNA polymerase δ (Pol δ), which takes over for Pol α to complete lagging-strand replication. When we compared MMR efficiency for errors made by variant forms of these two polymerases, Msh2-dependent repair efficiencies for mismatches made by Pol α were consistently higher than for those same mismatches when made by Pol δ. Thus, one special relationship between MMR and replication is that MMR is more efficient for the least accurate of the major replicative polymerases, exonuclease-deficient Pol α. This observation is consistent with the close proximity and possible use of 5′ ends of Okazaki fragments for strand discrimination, which could increase the probability of Msh2-dependent MMR by 5′ excision, by a Msh2-dependent strand displacement mechanism, or both.
Molecular architecture of the vesicular stomatitis virus RNA polymerase
Authors: Rahmeh Amal A. , Schenk Andreas D. , Danek Eric I. , Kranzusch Philip J. , Liang Bo , Walz Thomas , Whelan Sean P. J.
Published: November 2010

Nonsegmented negative-strand (NNS) RNA viruses initiate infection by delivering into the host cell a highly specialized RNA synthesis machine comprising the genomic RNA completely encapsidated by the viral nucleocapsid protein and associated with the viral polymerase. The catalytic core of this protein–RNA complex is a 250-kDa multifunctional large (L) polymerase protein that contains enzymatic activities for nucleotide polymerization as well as for each step of mRNA cap formation. Working with vesicular stomatitis virus (VSV), a prototype of NNS RNA viruses, we used negative stain electron microscopy (EM) to obtain a molecular view of L, alone and in complex with the viral phosphoprotein (P) cofactor. EM analysis, combined with proteolytic digestion and deletion mapping, revealed the organization of L into a ring domain containing the RNA polymerase and an appendage of three globular domains containing the cap-forming activities. The capping enzyme maps to a globular domain, which is juxtaposed to the ring, and the cap methyltransferase maps to a more distal and flexibly connected globule. Upon P binding, L undergoes a significant rearrangement that may reflect an optimal positioning of its functional domains for transcription. The structural map of L provides new insights into the interrelationship of its various domains, and their rearrangement on P binding that is likely important for RNA synthesis. Because the arrangement of conserved regions involved in catalysis is homologous, the structural insights obtained for VSV L likely extend to all NNS RNA viruses.
Stepwise loading of yeast clamp revealed by ensemble and single-molecule studies
Authors: Kumar Ravindra , Nashine Vishal C. , Mishra Padmaja P. , Benkovic Stephen J. , Lee Tae-Hee
Published: November 2010

In ensemble and single-molecule experiments using the yeast proliferating cell nuclear antigen (PCNA, clamp) and replication factor C (RFC, clamp loader), we have examined the assembly of the RFC·PCNA·DNA complex and its progression to holoenzyme upon addition of polymerase δ (polδ). We obtained data that indicate (
i
) PCNA loading on DNA proceeds through multiple conformational intermediates and is successful after several failed attempts; (
ii
) RFC does not act catalytically on a primed 45-mer templated fork; (
iii
) the RFC·PCNA·DNA complex formed in the presence of ATP is derived from at least two kinetically distinguishable species; (
iv
) these species disassemble through either unloading of RFC·PCNA from DNA or dissociation of PCNA into its component subunits; and (
v
) in the presence of polδ only one species converts to the RFC·PCNA·DNA·pol
δ
holoenzyme. These findings redefine and deepen our understanding of the clamp-loading process and reveal that it is surprisingly one of trial and error to arrive at a heuristic solution.
Identification of the gene cluster for the dithiolopyrrolone antibiotic holomycin in
Streptomyces clavuligerus
Authors: Li Bo , Walsh Christopher T.
Published: November 2010

Streptomyces clavuligerus
, an industrially important producer of clavulanate as well as cephem antibiotics, also produces the N-acylated dithiolopyrrolone antibiotic holomycin, a reported inhibitor of RNA synthesis. The genome sequence of
S. clavuligerus
ATCC 27064 was examined for a potential biosynthetic gene cluster, assuming that holomycin arises from some derivative of an
l
-Cys-
l
-Cys dipeptide that has undergone eight-electron oxidation, fused five-five ring formation, and decarboxylation. ORFs 3483–3492 comprise a candidate cluster, with a predicted acyltransferase, a stand-alone nonribosomal peptide synthetase (NRPS) module, and four flavin-dependent oxidoreductases. Deletions of ORF3488, the NRPS module, and ORF3489, a phosphopantothenoylcysteine decarboxylase homolog, abolished holomycin production both in wild type and in a holomycin-overproducing mutant. Heterologous expression and purification of ORF3488 allowed demonstration of
l
-Cys-AMP formation and subsequent covalent tethering of Cys to the phosphopantetheinyl arm of the thiolation domain of this NRPS protein. Purified ORF3483 shows acyltransferase activity, converting holothin to holomycin and longer acylated homologs as the last step in antibiotic assembly.
Experimental human cytomegalovirus latency in CD14+monocytes
Authors: Hargett Danna , Shenk Thomas E.
Published: November 2010

CD14+monocytes are a reservoir for latent human cytomegalovirus, and virus replication is reactivated during their differentiation to macrophages or dendritic cells. It has not been clear whether the virus can establish latency upon direct infection of monocytes or whether it must first become quiescent in a progenitor cell that subsequently differentiates to generate a monocyte. We report that infection of primary human monocytes with a clinical strain of human cytomegalovirus exhibits the hallmarks of latency. We established conditions for culturing monocytes that prevent differentiation for at least 25 d, as evidenced by cell surface marker expression. Infection of these monocytes with the FIX clinical strain resulted in transient accumulation of many viral lytic RNAs and sustained expression of four previously described latency-associated transcripts. The amount of viral DNA remained constant after infection, and cell surface and total HLA-DR proteins were substantially reduced on a continuing basis after infection. When treated with cytokine mixtures that stimulate differentiation to a macrophage or dendritic cell phenotype, infected monocytes reactivated virus replication and produced infectious progeny. Treatment of infected monocytes with IL-6 alone also was sufficient for reactivation, and the particles produced after exposure to this cytokine were about fivefold more infectious than virions produced by other treatments. We propose that in vivo microenvironments influence not only the efficiency of reactivation but also the infectivity of the virions produced from latently infected monocytes.
A requirement for Lim domain binding protein 1 in erythropoiesis
Authors: Li LiQi , Lee Jan Y. , Gross Jennifer , Song Sang-Hyun , Dean Ann , Love Paul E.
Published: November 2010

During erythrocyte development, the nuclear cofactor Lim domain binding protein 1 (Ldb1) functions as a core subunit of multiprotein DNA binding complexes that include the transcription factors Scl and Gata-1 and the Lim-only adapter Lmo2. Scl, Gata-1, and Lmo2 are each required for erythropoiesis, suggesting that Ldb1-nucleated transcription complexes regulate key steps during erythropoiesis. We documented a requirement for Ldb1 in erythropoiesis in mice. Analysis of ldb1−/− embryos revealed a critical requirement for Ldb1 during primitive erythropoiesis, and conditional inactivation of ldb1 at later stages of gestation and in adult mice demonstrated that Ldb1 is continuously required for both definitive erythropoiesis and megakaryopoiesis. Down-regulation of Ldb1 in erythroblasts inhibited the expression of multiple erythroid-specific and prosurvival genes. These results represent the first unequivocal demonstration of a role for Ldb1 in erythropoiesis in vivo and establish a critical function for Ldb1-nucleated complexes in regulating the erythroid/megakaryocyte transcriptional program.
Regulation of activation-induced deaminase stability and antibody gene diversification by Hsp90
Authors: Orthwein Alexandre , Patenaude Anne-Marie , Affar El Bachir , Lamarre Alain , Young Jason C. , Di Noia Javier M.
Published: November 2010

Activation-induced deaminase (AID) is the mutator enzyme that initiates somatic hypermutation and isotype switching of the antibody genes in B lymphocytes. Undesired byproducts of AID function are oncogenic mutations. AID expression levels seem to correlate with the extent of its physiological and pathological functions. In this study, we identify AID as a novel Hsp90 (heat shock protein 90 kD) client. We find that cytoplasmic AID is in a dynamic equilibrium regulated by Hsp90. Hsp90 stabilizes cytoplasmic AID, as specific Hsp90 inhibition leads to cytoplasmic polyubiquitination and proteasomal degradation of AID. Consequently, Hsp90 inhibition results in a proportional reduction in antibody gene diversification and off-target mutation. This evolutionarily conserved regulatory mechanism determines the functional steady-state levels of AID in normal B cells and B cell lymphoma lines. Thus, Hsp90 assists AID-mediated antibody diversification by stabilizing AID. Hsp90 inhibition provides the first pharmacological means to down-regulate AID expression and activity, which could be relevant for therapy of some lymphomas and leukemias.
Blow-up rate of type II and the braid group theory
Authors: Mizoguchi Noriko
Published: November 2010

A solution

u
u

of a Cauchy problem or a Cauchy-Dirichlet problem for a semilinear heat equation
\[

u
t

=
Δ
u
+

u
p

u_t = \Delta u + u^p

\]
with nonnegative initial data

u
0

u_0

is said to undergo type II blow-up at

t
=
T

t = T

if
\[
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="limit sup left-parenthesis upper T minus t right-parenthesis Superscript 1 slash left-parenthesis p minus 1 right-parenthesis Baseline StartAbsoluteValue u left-parenthesis t right-parenthesis EndAbsoluteValue Subscript normal infinity Baseline equals normal infinity period">

lim sup

t
↗
T

(
T
−
t

)

1

/

(
p
−
1
)

|

u
(
t
)

|

∞

=
∞
.

\limsup _{t \nearrow T} \; (T-t)^{1/(p-1)} |u(t)|_\infty = \infty .

\]
Let

φ
∞

\varphi _\infty

be the radially symmetric singular steady state of the Cauchy problem. Suppose that

u
0

∈

L
∞

u_0 \in L^\infty

is a radially symmetric function such that

u
0

−

φ
∞

u_0 - \varphi _\infty

and

(

u
0

)
t

(u_0)_t

change sign at most finitely many times. By application of the braid group theory, we determine the exact blow-up rate of solution with initial data

u
0

u_0

which undergoes type II blow-up in the case of

p
>

p

J
L

p > p_{_{JL}}

, where

p

J
L

p_{_{JL}}

is the exponent of Joseph and Lundgren.