bluuebunny/crossref_metadata_2025 huggingface dataset:
Urbanization effects in large‐scale temperature records, with an emphasis on China
Authors: Jones P. D. , Lister D. H. , Li Q.
Published: August 2008

Global surface temperature trends, based on land and marine data, show warming of about 0.8°C over the last 100 years. This rate of warming is sometimes questioned because of the existence of well‐known Urban Heat Islands (UHIs). We show examples of the UHIs at London and Vienna, where city center sites are warmer than surrounding rural locations. Both of these UHIs however do not contribute to warming trends over the 20th century because the influences of the cities on surface temperatures have not changed over this time. In the main part of the paper, for China, we compare a new homogenized station data set with gridded temperature products and attempt to assess possible urban influences using sea surface temperature (SST) data sets for the area east of the Chinese mainland. We show that all the land‐based data sets for China agree exceptionally well and that their residual warming compared to the SST series since 1951 is relatively small compared to the large‐scale warming. Urban‐related warming over China is shown to be about 0.1°C decade−1 over the period 1951–2004, with true climatic warming accounting for 0.81°C over this period.
In situ determination of atmospheric aerosol composition as a function of hygroscopic growth
Authors: Herich Hanna , Kammermann Lukas , Gysel Martin , Weingartner Ernest , Baltensperger Urs , Lohmann Ulrike , Cziczo Daniel J.
Published: August 2008

An in situ measurement setup to determine the chemical composition of aerosols as a function of hygroscopicity is presented. This has been done by connecting a custom‐built Hygroscopicity Tandem Differential Mobility Analyzer (HTDMA) and an Aerosol Time‐of‐Flight Mass Spectrometer (ATOFMS), commercially available from TSI (Model 3800). Single particle bipolar mass spectra from aerosols leaving the HTDMA could thus be obtained as a function of the hygroscopic growth factor. For these studies the HTDMA was set at a relative humidity of 82% and particles with a dry diameter of 260 nm were selected. The setup was first laboratory tested, after which field experiments were performed. Two data sets were obtained during wintertime 2007 in Switzerland: the first in the urban Zurich environment and the other at the remote high alpine research station Jungfraujoch (JFJ). In Zurich, several thousand mass spectra were obtained in less than 2 days of sampling due to a high aerosol loading. At the JFJ, due to low particle concentrations in free tropospheric air masses, a longer sampling period was required. Both in Zurich and at the JFJ, two different growth factor modes were observed. Results from these two locations show that most aerosol particles were a mixture of several compounds. A large contribution of organics and combustion species was found in the less hygroscopic growth mode for both locations. Noncombustion refractory material (e.g., metals, mineral dust, and fly ash) was also highly enhanced in the nonhygroscopic particles. Sulfate, normally considered highly soluble, was found to be a constituent in almost all particles independent of their hygroscopic growth factor.
Predicting light penetration into river waters
Authors: Davies‐Colley Robert J. , Nagels John W.
Published: August 2008

Lighting in rivers often needs to be quantified, particularly for modeling benthic plant growth, but is seldom measured because of difficulties associated with limited depth and strong currents. Therefore, methods for predicting light attenuation from river water quality data would be very useful. We used measurements of the diffuse light attenuation coefficient, Kd (m−1), at 17 optically diverse rivers in New Zealand to develop simple empirical models of light penetration as functions of the beam attenuation coefficient at 550 nm, c550 (m−1, an index of visual water clarity) and the light absorption coefficient of membrane filtrates at 340 nm, g340 (m−1, an index of colored dissolved organic matter). The beam attenuation coefficient can be measured by beam transmissometer or estimated, as in this study, from black disc visibility observations. Alternatively, nephelometric turbidity, Tn (an index of light scattering), which is more commonly measured in water quality monitoring programs, can be used to predict Kd. The models performed satisfactorily when tested over a wide range of optical water quality (varying with flow) at one river site. We expect that these empirical models will have wide practical application for estimating light availability in rivers and streams.
The influence of carbon sources on recombinant‐human‐ growth‐hormone production by Pichia pastoris is dependent on phenotype: a comparison of Muts and Mut+ strains
Authors: Orman Mehmet Ali , Çalık Pınar , Özdamar Tunçer H.
Published: September 2008

The influence of carbon sources on rhGH (recombinant human growth hormone) production by two Pichia pastoris strains having different methanol utilization phenotypes (P. pastoris‐hGH‐Mut+ and P. pastoris‐hGH‐Muts) was investigated using batch bioreactors. The effect of methanol concentration (CMeOH) in defined and complex media, and further glycerol/methanol mixed defined media, was analysed systematically over a wide range. With methanol as the sole carbon source, strain Muts grew only slightly, whereas with Mut+, a cell concentration (CX) of 6.0 g of dry cells/dm3 was obtained and an rhGH concentration (CrhGH) of 0.032 g/dm3 was produced. In complex medium without glycerol at a CMeOH of 2% (v/v), a CrhGH of 0.16 g of rhGH/dm3 was produced by Muts, a value 3‐fold higher than that produced by Mut+, despite the fact that the CX of Mut+ (6.1 g/dm3) was 2‐fold higher than that of Muts (3.0 g/dm3). In a glycerol/methanol mixed defined medium, methanol consumption began when glycerol was totally depleted, indicating that glycerol is a repressor of the AOX1 (alcohol oxidase‐1 gene) promoter. With strain Muts at a glycerol concentration (CGly) of 30 g/dm3 and a CMeOH of 1% (v/v), the CrhGH produced was 0.11 g/dm3, whereas, with the Mut+ strain, a CrhGH of 0.06 g/dm3 was obtained at a CGly of 30 g/dm3 and a CMeOH of 4%. As methanol is not consumed by Muts strain effectively and the presence of methanol in the fermentation broth triggers induction of the AOX1 promoter, our results encourage the use of the Muts strain for rhGH production. In addition to rhGH production, the specific cell growth rates, specific methanol and/or glycerol utilization rates and maintenance coefficients in methanol‐ and glycerol‐based defined media were determined. With a methanol‐based defined medium and using the Mut+ strain, a higher specific growth rate (μ) of approx. 0.14 h−1 was observed during the exponential cell growth phase at a CMeOH of ≤2.0%. When glycerol was used as a sole carbon source, both phenotypes showed similar cell‐growth and glycerol‐utilization rates. The results of the present study should enable one to optimize the expression of other therapeutic proteins by P. pastoris.
Unfolding a codimension-two, discontinuous, Andronov–Hopf bifurcation
Authors: Simpson D. J. W. , Meiss J. D.
Published: August 2008

We present an unfolding of the codimension-two scenario of the simultaneous occurrence of a discontinuous bifurcation and an Andronov–Hopf bifurcation in a piecewise-smooth, continuous system of autonomous ordinary differential equations in the plane. We find that the Hopf cycle undergoes a grazing bifurcation that may be very shortly followed by a saddle-node bifurcation of the orbit. We derive scaling laws for the bifurcation curves that emanate from the codimension-two bifurcation.
Appearance of an Illusory Object in the Blind Spot
Authors: Araragi Yukyu , Ito Hiroyuki , Sunaga Shoji
Published: September 2008

We report a phenomenon showing new aspects of perceptual filling-in at the blind spot. When two and three discs were presented below the blind spot, observers perceived them as three and four discs, respectively, but when they were presented in the nasal visual field as a control, the perceived numbers were veridical. The phenomenon demonstrates that the visual system produces an illusory object in the blind spot even when the inducing objects presented on only one side of the blind spot are clearly discrete and countable.
Structural basis for the catalytic mechanism of human phosphodiesterase 9
Authors: Liu Shenping , Mansour Mahmoud N. , Dillman Keith S. , Perez Jose R. , Danley Dennis E. , Aeed Paul A. , Simons Samuel P. , LeMotte Peter K. , Menniti Frank S.
Published: August 2008

The phosphodiesterases (PDEs) are metal ion-dependent enzymes that regulate cellular signaling by metabolic inactivation of the ubiquitous second messengers cAMP and cGMP. In this role, the PDEs are involved in many biological and metabolic processes and are proven targets of successful drugs for the treatments of a wide range of diseases. However, because of the rapidity of the hydrolysis reaction, an experimental knowledge of the enzymatic mechanisms of the PDEs at the atomic level is still lacking. Here, we report the structures of reaction intermediates accumulated at the reaction steady state in PDE9/crystal and preserved by freeze-trapping. These structures reveal the catalytic process of a PDE and explain the substrate specificity of PDE9 in an actual reaction and the cation requirements of PDEs in general.
RCS1, a substrate of APC/C, controls the metaphase to anaphase transition
Authors: Zhao Wei-meng , Coppinger Judith A. , Seki Akiko , Cheng Xiao-li , Yates John R. , Fang Guowei
Published: August 2008

The anaphase-promoting complex/cyclosome (APC/C) controls the onset of anaphase by targeting securin for destruction. We report here the identification and characterization of a substrate of APC/C, RCS1, as a mitotic regulator that controls the metaphase-to-anaphase transition. We showed that the levels of RCS1 fluctuate in the cell cycle, peaking in mitosis and dropping drastically as cells exit into G
1
. Indeed, RCS1 is efficiently ubiquitinated by APC/C
in vitro
and degraded during mitotic exit in a Cdh1-dependent manner
in vivo
. APC/C recognizes a unique D-box at the N terminus of RCS1, as mutations of this D-box abolished ubiquitination
in vitro
and stabilized the mutant protein
in vivo
. RCS1 controls the timing of the anaphase onset, because the loss of RCS1 resulted in a faster progression from the metaphase to anaphase and accelerated degradation of securin and cyclin B. Biochemically, mitotic RCS1 associates with the NuRD chromatin-remodeling complex, and this RCS1 complex is likely involved in regulating gene expression or chromatin structure, which in turn may control anaphase onset. Our study uncovers a complex regulatory network for the metaphase-to-anaphase transition.
Correction of a splice-site mutation in the beta-globin gene stimulated by triplex-forming peptide nucleic acids
Authors: Chin Joanna Y. , Kuan Jean Y. , Lonkar Pallavi S. , Krause Diane S. , Seidman Michael M. , Peterson Kenneth R. , Nielsen Peter E. , Kole Ryszard , Glazer Peter M.
Published: August 2008

Splice-site mutations in the beta-globin gene can lead to aberrant transcripts and decreased functional beta-globin, causing beta-thalassemia. Triplex-forming DNA oligonucleotides (TFOs) and peptide nucleic acids (PNAs) have been shown to stimulate recombination in reporter gene loci in mammalian cells via site-specific binding and creation of altered helical structures that provoke DNA repair. We have designed a series of triplex-forming PNAs that can specifically bind to sequences in the human beta-globin gene. We demonstrate here that these PNAs, when cotransfected with recombinatory donor DNA fragments, can promote single base-pair modification at the start of the second intron of the beta-globin gene, the site of a common thalassemia-associated mutation. This single base pair change was detected by the restoration of proper splicing of transcripts produced from a green fluorescent protein-beta-globin fusion gene. The ability of these PNAs to induce recombination was dependent on dose, sequence, cell-cycle stage, and the presence of a homologous donor DNA molecule. Enhanced recombination, with frequencies up to 0.4%, was observed with use of the lysomotropic agent chloroquine. Finally, we demonstrate that these PNAs were effective in stimulating the modification of the endogenous beta-globin locus in human cells, including primary hematopoietic progenitor cells. This work suggests that PNAs can be effective tools to induce heritable, site-specific modification of disease-related genes in human cells.
Neuronal system-dependent facilitation of tumor angiogenesis and tumor growth by calcitonin gene-related peptide
Authors: Toda Masaya , Suzuki Tatsunori , Hosono Kanako , Hayashi Izumi , Hashiba Shinichiro , Onuma Yuichiro , Amano Hideki , Kurihara Yukiko , Kurihara Hiroki , Okamoto Hirotsugu , Hoka Sumio , Majima Masataka
Published: August 2008

A neuropeptide, calcitonin gene-related peptide (CGRP), is widely distributed in neuronal systems and exhibits numerous biological activities. Using CGRP-knockout mice (CGRP
−/−
), we examined whether or not endogenous CGRP facilitates angiogenesis indispensable to tumor growth. CGRP increased tube formation by endothelial cells
in vitro
and enhanced sponge-induced angiogenesis
in vivo
. Tumor growth and tumor-associated angiogenesis in CGRP
−/−
implanted with Lewis lung carcinoma (LLC) cells were significantly reduced compared with those in wild-type (WT) mice. A CGRP antagonist, CGRP8-37 or denervation of sciatic nerves (L
1–5
) suppressed LLC growth in the sites of denervation compared with vehicle infusion or sham operation. CGRP precursor mRNA levels in the dorsal root ganglion in LLC-bearing WT were increased compared with those in non-LLC-bearing mice. This increase was abolished by denervation. The expression of VEGF in tumor stroma was down-regulated in CGRP
−/−
. These results indicate that endogenous CGRP facilitates tumor-associated angiogenesis and tumor growth and suggest that relevant CGRP may be derived from neuronal systems including primary sensory neurons and may become a therapeutic target for cancers.
Theory of solvatochromic shifts in nonpolar solvents reveals a new spectroscopic rule
Authors: Renger Thomas , Grundkötter Bernhard , Madjet Mohamed El-Amine , Müh Frank
Published: August 2008

An expression of unexpected simplicity is derived for the shift in optical transition energies of solute molecules in nonpolar solvents. The expression reveals a new spectroscopic rule that says: The higher the excited state of the solute, the larger the solvatochromic red shift. A puzzle formulated >50 years ago by Bayliss is solved. Bayliss, based on arguments from classical physics, assumed that the shift scales with the oscillator strength of the solute transition, but noted strong quantitative deviations from this rule in experiments. As the present expression shows, the shift does not depend on the oscillator strength of the transition, but reflects the change in dispersive solute–solvent interactions between the ground and excited states of the solute, that are determined by the anisotropy of intramolecular electron correlation. The theory is applied to explain the solvatochromic shifts of the two lowest electronic excitations of bacteriochlorophyll
a
and bacteriopheophytin
a
.
Built-in loops allow versatility in domain–domain interactions: Lessons from self-interacting domains
Authors: Akiva Eyal , Itzhaki Zohar , Margalit Hanah
Published: August 2008

Compilations of domain–domain interactions based on solved structures suggest there are distinct domain pairs that are used repeatedly in different protein contexts to mediate protein–protein interactions. However, not all protein pairs with the corresponding domains that can potentially mediate interaction do interact, even when they are colocalized and coexpressed. It is conceivable that there are structural and sequence features, below the domain level, that play a role in determining the potential of domains to mediate protein–protein interactions. Here, we discover such features by comparing domains that, on the one hand, mediate homodimerization of proteins and, on the other, occur in different proteins that are documented as monomers. Intriguingly, this comparison uncovered surface loops that can be considered as determinants of the interactions. There are enabling loops, which mediate the domain interactions, and disabling loops that prevent the interactions. The presence of the enabling/disabling loops is consistent with the fulfillment/prevention of the interaction and is highly preserved in evolution. This suggests that, along with the preservation of structural elements that enable interaction, evolution maintains elements intended to prevent unwanted interactions. The enabling and disabling loops discovered in this study have implications in prediction of protein–protein interactions, by pointing to the protein regions that determine the interaction. Our results extend the hierarchy of attributes that collectively establish the modularity of domain-mediated protein–protein interactions.
A conserved salt bridge critical for GABAAreceptor function and loop C dynamics
Authors: Venkatachalan Srinivasan P. , Czajkowski Cynthia
Published: August 2008

Chemical signaling in the brain involves rapid opening and closing of ligand gated ion channels (LGICs). LGICs are allosteric membrane proteins that transition between multiple conformational states (closed, open, and desensitized) in response to ligand binding. While structural models of cys-loop LGICs have been recently developed, our understanding of the protein movements underlying these conformational transitions is limited. Neurotransmitter binding is believed to initiate an inward capping movement of the loop C region of the ligand-binding site, which ultimately triggers channel gating. Here, we identify a critical intrasubunit salt bridge between conserved charged residues (βE153, βK196) in the GABAAreceptor (GABAAR) that is involved in regulating loop C position. Charge reversals (E153K, K196E) increased the EC50for GABA and for the allosteric activators pentobarbital (PB) and propofol indicating that these residues are critical for channel activation, and charge swap (E153K-K196E) significantly rescued receptor function suggesting a functional electrostatic interaction. Mutant cycle analysis of alanine substitutions indicated that E153 and K196 are energetically coupled. By monitoring disulfide bond formation between cysteines substituted at these positions (E153C-K196C), we probed the mobility of loop C in resting and ligand-bound states. Disulfide bond formation was significantly reduced in the presence of GABA or PB suggesting that agonist activation of the GABAAR proceeds via restricting loop C mobility.
Characterization of the proteasome interaction network using a QTAX-based tag-team strategy and protein interaction network analysis
Authors: Guerrero Cortnie , Milenković Tijana , Pržulj Nataša , Kaiser Peter , Huang Lan
Published: August 2008

Quantitative analysis of tandem-affinity purified cross-linked (
x
) protein complexes (QTAX) is a powerful technique for the identification of protein interactions, including weak and/or transient components. Here, we apply a QTAX-based tag-team mass spectrometry strategy coupled with protein network analysis to acquire a comprehensive and detailed assessment of the protein interaction network of the yeast 26S proteasome. We have determined that the proteasome network is composed of at least 471 proteins, significantly more than the total number of proteins identified by previous reports using proteasome subunits as baits. Validation of the selected proteasome-interacting proteins by reverse copurification and immunoblotting experiments with and without cross-linking, further demonstrates the power of the QTAX strategy for capturing protein interactions of all natures. In addition, >80% of the identified interactions have been confirmed by existing data using protein network analysis. Moreover, evidence obtained through network analysis links the proteasome to protein complexes associated with diverse cellular functions. This work presents the most complete analysis of the proteasome interaction network to date, providing an inclusive set of physical interaction data consistent with physiological roles for the proteasome that have been suggested primarily through genetic analyses. Moreover, the methodology described here is a general proteomic tool for the comprehensive study of protein interaction networks.
Effects of denaturants and osmolytes on proteins are accurately predicted by the molecular transfer model
Authors: O'Brien Edward P. , Ziv Guy , Haran Gilad , Brooks Bernard R. , Thirumalai D.
Published: August 2008

Interactions between denaturants and proteins are commonly used to probe the structures of the denatured state ensemble and their stabilities. Osmolytes, a class of small intracellular organic molecules found in all taxa, also profoundly affect the equilibrium properties of proteins. We introduce the molecular transfer model, which combines simulations in the absence of denaturants or osmolytes, and Tanford's transfer model to predict the dependence of equilibrium properties of proteins at finite concentration of osmolytes. The calculated changes in the thermodynamic quantities (probability of being in the native basin of attraction,
m
values, FRET efficiency, and structures of the denatured state ensemble) with GdmCl concentration [C] for the protein L and cold shock protein CspTm compare well with experiments. The radii of gyration of the subpopulation of unfolded molecules for both proteins decrease (i.e., they undergo a collapse transition) as [C] decreases. Although global folding is cooperative, residual secondary structures persist at high denaturant concentrations. The temperature dependence of the specific heat shows that the folding temperature (
T
F
) changes linearly as urea and trimethylamine
N
-oxide (TMAO) concentrations increase. The increase in
T
F
in TMAO can be as large as 20°C, whereas urea decreases
T
F
by as much as 35°C. The stabilities of protein L and CspTm also increase linearly with the concentration of osmolytes (proline, sorbitol, sucrose, TMAO, and sarcosine).
Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified
Authors: Song Hojun , Buhay Jennifer E. , Whiting Michael F. , Crandall Keith A.
Published: August 2008

Nuclear mitochondrial pseudogenes (numts) are nonfunctional copies of mtDNA in the nucleus that have been found in major clades of eukaryotic organisms. They can be easily coamplified with orthologous mtDNA by using conserved universal primers; however, this is especially problematic for DNA barcoding, which attempts to characterize all living organisms by using a short fragment of the mitochondrial cytochromecoxidase I (COI) gene. Here, we study the effect of numts on DNA barcoding based on phylogenetic and barcoding analyses of numt and mtDNA sequences in two divergent lineages of arthropods: grasshoppers and crayfish. Single individuals from both organisms have numts of the COI gene, many of which are highly divergent from orthologous mtDNA sequences, and DNA barcoding analysis incorrectly overestimates the number of unique species based on the standard metric of 3% sequence divergence. Removal of numts based on a careful examination of sequence characteristics, including indels, in-frame stop codons, and nucleotide composition, drastically reduces the incorrect inferences of the number of unique species, but even such rigorous quality control measures fail to identify certain numts. We also show that the distribution of numts is lineage-specific and the presence of numts cannot be knowna priori. Whereas DNA barcoding strives for rapid and inexpensive generation of molecular species tags, we demonstrate that the presence of COI numts makes this goal difficult to achieve when numts are prevalent and can introduce serious ambiguity into DNA barcoding.
The
Pseudomonas aeruginosa
multidrug efflux regulator MexR uses an oxidation-sensing mechanism
Authors: Chen Hao , Hu Jie , Chen Peng R. , Lan Lefu , Li Zigang , Hicks Leslie M. , Dinner Aaron R. , He Chuan
Published: August 2008

MexR is a MarR family protein that negatively regulates multidrug efflux systems in the human pathogen
Pseudomonas aeruginosa
. The mechanism of MexR-regulated antibiotic resistance has never been elucidated in the past. We present here that two Cys residues in MexR are redox-active. They form intermonomer disulfide bonds in MexR dimer with a redox potential of −155 mV. This MexR oxidation leads to its dissociation from promoter DNA, derepression of the
mexAB–oprM
drug efflux operon, and increased antibiotic resistance of
P. aeruginosa
. We show computationally that the formation of disulfide bonds is consistent with a conformation change that prevents the oxidized MexR from binding to DNA. Collectively, the results reveal that MexR is a redox regulator that senses peroxide stress to mediate antibiotic resistance in
P. aeruginosa
.
Mate choice for more melanin as a mechanism to maintain a functional oncogene
Authors: Fernandez André A. , Morris Molly R.
Published: August 2008

The mechanisms by which cancer evolves and persists in natural systems have been difficult to ascertain. In theXiphophorusmelanoma model, a functional oncogene (Xiphophorusmelanoma receptor kinaseXmrk) has been maintained for several million years despite being deleterious and in an extremely unstable genomic region. Melanomas inXiphophorus spp.fishes (platyfishes and swordtails) have been investigated since the 1920s, and, yet, positive selection that could explain the maintenance ofXmrkhas not been found. Here, we show thatXiphophorus cortezifemales from two populations prefer males with the spotted caudal (Sc) melanin pattern, which is associated with the presence of theXmrkoncogene and serves as the site of melanoma formation within this species. Moreover,X. cortezifemales prefer males with an enhanced Sc to males with a reduced Sc pattern. RT-PCR analysis confirms tissue-specificXmrkexpression within the Sc pattern inX. cortezi. Because of the association ofXmrkwith the Sc pigment pattern and the fact that melanoma formation augments this visual signal, sexual selection appears to be maintaining this oncogene because of a mating preference for Sc, as well as the exaggeration of this male trait. At the individual level, decreases in viability and fecundity because ofXmrkand subsequent melanoma formation may be mitigated via increases in mate acquisition. At the population level, maintenance of this oncogene appears to be under frequency dependent selection, as we detected female preference for males without Sc in a third population that had higher frequencies of Sc in females.
Toxoplasma gondii
Tic20 is essential for apicoplast protein import
Authors: van Dooren Giel G. , Tomova Cveta , Agrawal Swati , Humbel Bruno M. , Striepen Boris
Published: August 2008

Apicomplexan parasites harbor a secondary plastid that has lost the ability to photosynthesize yet is essential for the parasite to multiply and cause disease. Bioinformatic analyses predict that 5–10% of all proteins encoded in the parasite genome function within this organelle. However, the mechanisms and molecules that mediate import of such large numbers of cargo proteins across the four membranes surrounding the plastid remain elusive. In this work, we identify a highly diverged member of the Tic20 protein family in Apicomplexa. We demonstrate that Tic20 of
Toxoplasma gondii
is an integral protein of the innermost plastid membrane. We engineer a conditional null-mutant and show that
Tg
Tic20 is essential for parasite growth. To characterize this mutant functionally, we develop several independent biochemical import assays to reveal that loss of
Tg
Tic20 leads to severe impairment of apicoplast protein import followed by organelle loss and parasite death.
Tg
Tic20 is the first experimentally validated protein import factor identified in apicoplasts. Our studies provide experimental evidence for a common evolutionary origin of import mechanisms across the innermost membranes of primary and secondary plastids.
The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning
Authors: Wilson Daniel N. , Schluenzen Frank , Harms Joerg M. , Starosta Agata L. , Connell Sean R. , Fucini Paola
Published: August 2008

The oxazolidinones represent the first new class of antibiotics to enter into clinical usage within the past 30 years, but their binding site and mechanism of action has not been fully characterized. We have determined the crystal structure of the oxazolidinone linezolid bound to theDeinococcus radiodurans50S ribosomal subunit. Linezolid binds in the A site pocket at the peptidyltransferase center of the ribosome overlapping the aminoacyl moiety of an A-site bound tRNA as well as many clinically important antibiotics. Binding of linezolid stabilizes a distinct conformation of the universally conserved 23S rRNA nucleotide U2585 that would be nonproductive for peptide bond formation. In conjunction with available biochemical data, we present a model whereby oxazolidinones impart their inhibitory effect by perturbing the correct positioning of tRNAs on the ribosome.
Communication-induced memory biases in preverbal infants
Authors: Yoon Jennifer M. D. , Johnson Mark H. , Csibra Gergely
Published: August 2008

Human teaching, a highly specialized form of cooperative information transmission, depends not only on the presence of benevolent communicators in the environment, but also on the preparedness of the students to learn from communication when it is addressed to them. We tested whether 9-month-old human infants can distinguish between communicative and noncommunicative social contexts and whether they retain qualitatively different information about novel objects in these contexts. We found that in a communicative context, infants devoted their limited memory resources to encoding the identity of novel objects at the expense of encoding their location, which is preferentially retained in noncommunicative contexts. We propose that infants' sensitivity to, and interpretation of, the social cues distinguishing infant-directed communication events represent important mechanisms of social learning by which others can help determine what information even preverbal human observers retain in memory.
Compartmentation and compartment-specific regulation of PDE5 by protein kinase G allows selective cGMP-mediated regulation of platelet functions
Authors: Wilson Lindsay S. , Elbatarny Hisham S. , Crawley Scott W. , Bennett Brian M. , Maurice Donald H.
Published: August 2008

It is generally accepted that nitric oxide (NO) donors, such as sodium nitroprusside (SNP), or phosphodiesterase 5 (PDE5) inhibitors, including sildenafil, each impact human platelet function. Although a strong correlation exists between the actions of NO donors in platelets and their impact on cGMP, agents such as sildenafil act without increasing global intra-platelet cGMP levels. This study was undertaken to identify how PDE5 inhibitors might act without increasing cGMP. Our data identify PDE5 as an integral component of a protein kinase G1β (PKG1β)-containing signaling complex, reported previously to coordinate cGMP-mediated inhibition of inositol-1, 4, 5-trisphosphate receptor type 1 (IP3R1)-mediated Ca2+-release. PKG1β and PDE5 did not interact in subcellular fractions devoid of IP3R1 and were not recruited to IP3R1-enriched membranes in response to cGMP-elevating agents. Activation of platelet PKG promoted phosphorylation and activation of the PDE5 fraction tethered to the IP3R1-PKG complex, an effect not observed for the nontethered PDE5. Based on these findings, we elaborate a model in which PKG selectively activates PDE5 within a defined microdomain in platelets and propose that this mechanism allows spatial and temporal regulation of cGMP signaling in these cells. Recent reports indicate that sildenafil might prove useful in limiting in-stent thrombosis and the thrombotic events associated with the acute coronary syndromes (ACS), situations poorly regulated with currently available therapeutics. We submit that our findings may define a molecular mechanism by which PDE5 inhibition can differentially impact selected cellular functions of platelets, and perhaps of other cell types.
A compromise required by gene sharing enables survival: Implications for evolution of new enzyme activities
Authors: McLoughlin Sean Yu , Copley Shelley D.
Published: August 2008

Evolution of new enzymatic activities is believed to require a period of gene sharing in which a single enzyme must serve both its original function and a new function that has become advantageous to the organism. Subsequent gene duplication allows one copy to maintain the original function, while the other diverges to optimize the new function. The physiological impact of gene sharing and the constraints imposed by the need to maintain the original activity during the early stages of evolution of a new activity have not been addressed experimentally. We report here an investigation of the evolution of a new activity under circumstances in which both the original and the new activity are critical for growth. Glutamylphosphate reductase (ProA) has a very low promiscuous activity with
N
-acetylglutamylphosphate, the normal substrate for ArgC (
N
-acetylglutamylphosphate reductase). A mutation that changes Glu-383 to Ala increases the promiscuous activity by 12-fold but decreases the original activity by 2,800-fold. The impairment in Pro and Arg synthesis results in 14-fold overexpression of E383A ProA, providing sufficient
N
-acetylglutamylphosphate reductase activity to allow a strain lacking ArgC to grow on glucose. Thus, reaching the threshold level of NAGP reductase activity required for survival required both a structural mutation and overexpression of the enzyme. Notably, overexpression does not require a mutation in the regulatory region of the protein; amino acid limitation attributable to the poor catalytic abilities of E383A ProA causes a physiological response that results in overexpression.
Enhanced photoprotection pathways in symbiotic dinoflagellates of shallow-water corals and other cnidarians
Authors: Reynolds Jennifer McCabe , Bruns Brigitte U. , Fitt William K. , Schmidt Gregory W.
Published: August 2008

Photoinhibition, exacerbated by elevated temperatures, underlies coral bleaching, but sensitivity to photosynthetic loss differs among various phylotypes of
Symbiodinium
, their dinoflagellate symbionts.
Symbiodinium
is a common symbiont in many cnidarian species including corals, jellyfish, anemones, and giant clams. Here, we provide evidence that most members of clade A
Symbiodinium
, but not clades B–D or F, exhibit enhanced capabilities for alternative photosynthetic electron-transport pathways including cyclic electron transport (CET). Unlike other clades, clade A
Symbiodinium
also undergo pronounced light-induced dissociation of antenna complexes from photosystem II (PSII) reaction centers. We propose these attributes promote survival of most cnidarians with clade A symbionts at high light intensities and confer resistance to bleaching conditions that conspicuously impact deeper dwelling corals that harbor non-clade A
Symbiodinium
.
Mechano-regulated Tenascin-C orchestrates muscle repair
Authors: Flück Martin , Mund Sonja I. , Schittny Johannes C. , Klossner Stephan , Durieux Anne-Cécile , Giraud Marie-Noëlle
Published: August 2008

Tenascin-C (TNC) is a mechano-regulated, morphogenic, extracellular matrix protein that is associated with tissue remodeling. The physiological role of TNC remains unclear because transgenic mice engineered for a TNC deficiency, via a defect in TNC secretion, show no major pathologies. We hypothesized that TNC-deficient mice would demonstrate defects in the repair of damaged leg muscles, which would be of functional significance because this tissue is subjected to frequent cycles of mechanical damage and regeneration. TNC-deficient mice demonstrated a blunted expression of the large TNC isoform and a selective atrophy of fast-muscle fibers associated with a defective, fast myogenic expression response to a damaging mechanical challenge. Transcript profiling mapped a set of de-adhesion, angiogenesis, and wound healing regulators as TNC expression targets in striated muscle. Expression of these regulators correlated with the residual expression of a damage-related 200-kDa protein, which resembled the small TNC isoform. Somatic knockin of TNC in fast-muscle fibers confirmed the activation of a complex expression program of interstitial and slow myofiber repair by myofiber-derived TNC. The results presented here show that a TNC-orchestrated molecular pathway integrates muscle repair into the load-dependent control of the striated muscle phenotype.
Neural predictors of moment-to-moment fluctuations in cognitive flexibility
Authors: Leber Andrew B. , Turk-Browne Nicholas B. , Chun Marvin M.
Published: August 2008

Cognitive flexibility is a crucial human ability allowing efficient adaptation to changing task challenges. Although a person's degree of flexibility can vary from moment to moment, the conditions regulating such fluctuations are not well understood. Using a task-switching procedure with fMRI, we found several brain regions in which neural activity preceding each trial predicted subsequent cognitive flexibility. Specifically, as pretrial activity increased, performance improved on trials when the task switched but did not improve when the task repeated. Regions from which flexibility could be predicted reliably included the basal ganglia, anterior cingulate cortex, prefrontal cortex, and posterior parietal cortex. Although further analysis revealed similarities across the regions in how flexibility was predicted, results supported the existence of multiple independent sources of prediction. These results reveal distinct neural mechanisms underlying fluctuations in cognitive flexibility.
Clozapine and sulpiride but not haloperidol or olanzapine activate brain DNA demethylation
Authors: Dong E. , Nelson M. , Grayson D. R. , Costa E. , Guidotti A.
Published: August 2008

Cortical GABAergic dysfunction, a hallmark of both schizophrenia (SZ) and bipolar (BP) disorder pathophysiologies may relate to the hypermethylation of GABAergic gene promoters (i.e., reelin and GAD67). Benefits elicited by a combination of atypical antipsychotics with valproate (VPA) (a histone deacetylase inhibitor that may also activate brain DNA demethylation) in SZ or BP disorder treatment prompted us to investigate whether the beneficial action of this association depends on induction of a putative DNA demethylase activity. To monitor this activity, we measured the ratio of 5-methyl cytosine to unmethylated cytosine in reelin and GAD67 promoters in the mouse frontal cortex and striatum. We compared normal mice with mice pretreated with
l
-methionine (5.2 mmol/kg s.c. twice a day for 7 days) to hypermethylate promoters, including reelin and GAD67. Clinically relevant doses of clozapine (CLZ) (3.8 to 15 μmol/kg twice a day s.c. for 3 days) and sulpiride (SULP) (12.5 to 50 μmol/kg twice a day for 3 days) but not clinically relevant doses of haloperidol (HAL) (1.3 to 4 μmol/kg twice a day s.c. for 3 days) or olanzapine (OLZ) (4 to 15 μmol/kg twice a day for 3 days) exhibited dose-related increases in the cortical and striatal demethylation of hypermethylated reelin and GAD67 promoters. These effects of CLZ and SULP were dramatically potentiated by a clinically relevant VPA dose (0.5 mmol/kg twice a day for 3 days). By activating a DNA demethylase, the association of CLZ or SULP with VPA may facilitate a chromatin remodeling that normalizes the GABAergic gene expression down-regulation detected in the telencephalic regions of SZ and BP patients.
Extraordinarily thick-boned fish linked to the aridification of the Qaidam Basin (northern Tibetan Plateau)
Authors: Chang Meemann , Wang Xiaoming , Liu Huanzhang , Miao Desui , Zhao Quanhong , Wu Guoxuan , Liu Juan , Li Qiang , Sun Zhencheng , Wang Ning
Published: August 2008

Scattered with numerous salt lakes and ≈2,700–3,200 m above sea level, the giant Qaidam inland basin on the northern Tibetan Plateau has experienced continuing aridification since the beginning of the Late Cenozoic as a result of the India–Asia plate collision and associated uplift of the Tibetan Plateau. Previous evidence of aridification comes mainly from evaporite deposits and salinity-tolerant invertebrate fossils. Vertebrate fossils were rare until recent discoveries of abundant fish. Here, we report an unusual cyprinid fish,Hsianwenia wui, gen. et sp. nov., from Pliocene lake deposits of the Qaidam Basin, characterized by an extraordinarily thick skeleton that occupied almost the entire body. Such enormous skeletal thickening, apparently leaving little room for muscles, is unknown among extant fish. However, an almost identical condition occurs in the much smaller cyprinodontidAphanius crassicaudus(Cyprinodonyiformes), collected from evaporites exposed along the northern margins of the Mediterranean Sea during the Messinian desiccation period.H. wuiandA. crassicaudusboth occur in similar deposits rich in carbonates (CaCO3) and sulfates (CaSO4), indicating that both were adapted to the extreme conditions resulting from the aridification in the two areas. The overall skeletal thickening was most likely formed through deposition of the oversaturated calcium and was apparently a normal feature of the biology and growth of these fish.
Numerical thought with and without words: Evidence from indigenous Australian children
Authors: Butterworth Brian , Reeve Robert , Reynolds Fiona , Lloyd Delyth
Published: August 2008

Are thoughts impossible without the words to express them? It has been claimed that this is the case for thoughts about numbers: Children cannot have the concept of exact numbers until they know the words for them, and adults in cultures whose languages lack a counting vocabulary similarly cannot possess these concepts. Here, using classical methods of developmental psychology, we show that children who are monolingual speakers of two Australian languages with very restricted number vocabularies possess the same numerical concepts as a comparable group of English-speaking indigenous Australian children.
The amyloid β-peptide is imported into mitochondria via the TOM import machinery and localized to mitochondrial cristae
Authors: Hansson Petersen Camilla A. , Alikhani Nyosha , Behbahani Homira , Wiehager Birgitta , Pavlov Pavel F. , Alafuzoff Irina , Leinonen Ville , Ito Akira , Winblad Bengt , Glaser Elzbieta , Ankarcrona Maria
Published: August 2008

The amyloid β-peptide (Aβ) has been suggested to exert its toxicity intracellularly. Mitochondrial functions can be negatively affected by Aβ and accumulation of Aβ has been detected in mitochondria. Because Aβ is not likely to be produced locally in mitochondria, we decided to investigate the mechanisms for mitochondrial Aβ uptake. Our results from rat mitochondria show that Aβ is transported into mitochondria via the translocase of the outer membrane (TOM) machinery. The import was insensitive to valinomycin, indicating that it is independent of the mitochondrial membrane potential. Subfractionation studies following the import experiments revealed Aβ association with the inner membrane fraction, and immunoelectron microscopy after import showed localization of Aβ to mitochondrial cristae. A similar distribution pattern of Aβ in mitochondria was shown by immunoelectron microscopy in human cortical brain biopsies obtained from living subjects with normal pressure hydrocephalus. Thus, we present a unique import mechanism for Aβ in mitochondria and demonstrate both
in vitro
and
in vivo
that Aβ is located to the mitochondrial cristae. Importantly, we also show that extracellulary applied Aβ can be internalized by human neuroblastoma cells and can colocalize with mitochondrial markers. Together, these results provide further insight into the mitochondrial uptake of Aβ, a peptide considered to be of major significance in Alzheimer's disease.
Cancer related mutations in
NRF2
impair its recognition by Keap1-Cul3 E3 ligase and promote malignancy
Authors: Shibata Tatsuhiro , Ohta Tsutomu , Tong Kit I. , Kokubu Akiko , Odogawa Reiko , Tsuta Koji , Asamura Hisao , Yamamoto Masayuki , Hirohashi Setsuo
Published: August 2008

The nuclear factor E2-related factor 2 (Nrf2) is a master transcriptional activator of genes encoding numerous cytoprotective enzymes that are induced in response to environmental and endogenously derived oxidative/electrophilic agents. Under normal, nonstressed circumstances, low cellular concentrations of Nrf2 are maintained by proteasomal degradation through a Keap1-Cul3-Roc1-dependent mechanism. A model for Nrf2 activation has been proposed in which two amino-terminal motifs, DLG and ETGE, promote efficient ubiquitination and rapid turnover; known as the two-site substrate recognition/hinge and latch model. Here, we show that in human cancer, somatic mutations occur in the coding region of
NRF2
, especially among patients with a history of smoking or suffering from squamous cell carcinoma; in the latter case, this leads to poor prognosis. These mutations specifically alter amino acids in the DLG or ETGE motifs, resulting in aberrant cellular accumulation of Nrf2. Mutant Nrf2 cells display constitutive induction of cytoprotective enzymes and drug efflux pumps, which are insensitive to Keap1-mediated regulation. Suppression of Nrf2 protein levels by siRNA knockdown sensitized cancer cells to oxidative stress and chemotherapeutic reagents. Our results strongly support the contention that constitutive Nrf2 activation affords cancer cells with undue protection from their inherently stressed microenvironment and anti-cancer treatments. Hence, inactivation of the Nrf2 pathway may represent a therapeutic strategy to reinforce current treatments for malignancy. Congruously, the present study also provides
in vivo
validation of the two-site substrate recognition model for Nrf2 activation by the Keap1-Cul3-based E3 ligase.
EGF receptor-independent action of TGF-α protects Naked2 from AO7-mediated ubiquitylation and proteasomal degradation
Authors: Ding Wei , Li Cunxi , Hu Tianhui , Graves-Deal Ramona , Fotia Andrew B. , Weissman Allan M. , Coffey Robert J.
Published: August 2008

Naked family members (
Drosophila Naked Cuticle
and mammalian Naked1 and Naked2) have been identified as inducible antagonists of canonical Wnt signaling. We recently reported that Naked2, but not Naked1, interacts with the cytoplasmic tail of TGF-α, thereby coating TGF-α-containing exocytic vesicles and directing these vesicles to the basolateral corner of polarized epithelial cells. Here, we show that Naked2 is a short-lived protein with a half-life of 60 min caused by its rapid ubiquitin-mediated proteasomal degradation. Overexpression of TGF-α stabilizes Naked2 protein in an EGF receptor (EGFR)-independent manner; a physical interaction between the cytoplasmic tail of TGF-α and Naked2 is necessary and sufficient for this protection. We have identified a RING finger protein, AO7/RNF25, as a ubiquitin ligase for Naked2, and we have shown that overexpression of TGF-α reduces binding of AO7 to Naked2. These results identify an EGFR-independent action of TGF-α, in which it protects Naked2 from proteasomal degradation, thus ensuring its delivery to the basolateral surface of polarized epithelial cells.