bluuebunny/crossref_metadata_2025 huggingface dataset:
Simple method of light-shift suppression in optical pumping systems
Authors: McGuyer B. H. , Jau Y.-Y. , Happer W.
Published: June 2009

We report a simple method to suppress the light shift in optical pumping systems. This method uses only frequency modulation of a radio frequency or microwave source, which is used to excite an atomic resonance, to simultaneously lock the source frequency to the atomic resonance and lock the pumping light frequency to suppress the light shift. We experimentally validate the method in a vapor-cell atomic clock and verify the results through numerical simulation. This technique can be applied to many optical pumping systems that experience light shifts. It is especially useful for atomic frequency standards because it improves long-term performance, reduces the influence of the laser, and requires less equipment than previous methods.
Mechanical properties of superhard BC5
Authors: Lazar P. , Podloucky R.
Published: June 2009

We apply density functional theory concept to investigate mechanical properties of the diamondlike compound BC5. The cell volume and the bulk modulus are in very good agreement with the experiment, confirming the claimed crystal structure of BC5. The cleavage properties revealed a very strong cohesion between B–C bonded planes, which is comparable to C–C bonded planes. The lowest cleavage stress, which can be related to hardness, is 83 GPa. The critical shear stresses are 83 and 108 GPa, respectively, for B–C and C–C planes. This difference of critical stresses corresponds well to the difference in Vickers hardness between BC5 and diamond.
Subseafloor sedimentary life in the South Pacific Gyre
Authors: D'Hondt Steven , Spivack Arthur J. , Pockalny Robert , Ferdelman Timothy G. , Fischer Jan P. , Kallmeyer Jens , Abrams Lewis J. , Smith David C. , Graham Dennis , Hasiuk Franciszek , Schrum Heather , Stancin Andrea M.
Published: June 2009

The low-productivity South Pacific Gyre (SPG) is Earth's largest oceanic province. Its sediment accumulates extraordinarily slowly (0.1–1 m per million years). This sediment contains a living community that is characterized by very low biomass and very low metabolic activity. At every depth in cored SPG sediment, mean cell abundances are 3 to 4 orders of magnitude lower than at the same depths in all previously explored subseafloor communities. The net rate of respiration by the subseafloor sedimentary community at each SPG site is 1 to 3 orders of magnitude lower than the rates at previously explored sites. Because of the low respiration rates and the thinness of the sediment, interstitial waters are oxic throughout the sediment column in most of this region. Consequently, the sedimentary community of the SPG is predominantly aerobic, unlike previously explored subseafloor communities. Generation of H
2
by radiolysis of water is a significant electron-donor source for this community. The per-cell respiration rates of this community are about 2 orders of magnitude higher (in oxidation/reduction equivalents) than in previously explored anaerobic subseafloor communities. Respiration rates and cell concentrations in subseafloor sediment throughout almost half of the world ocean may approach those in SPG sediment.
Genomic–anatomic evidence for distinct functional domains in hippocampal field CA1
Authors: Dong Hong-Wei , Swanson Larry W. , Chen Lin , Fanselow Michael S. , Toga Arthur W.
Published: June 2009

Functional heterogeneity has been investigated for decades in the hippocampal region of the mammalian cerebral cortex, and evidence for vaguely defined “dorsal” and “ventral” regions is emerging. Direct evidence that hippocampal field CA1 displays clear regional, laminar, and pyramidal neuron differentiation is presented here, based on a systematic high-resolution analysis of a publicly accessible, genome-wide expression digital library (Allen Brain Atlas) [Lein et al. (2007) Genome-wide atlas of gene expression in the adult mouse brain.
Nature
445:168–176]. First, genetic markers reveal distinct spatial expression domains and subdomains along the longitudinal (dorsal/septal/posterior to ventral/temporal/anterior) axis of field CA1. Second, genetic markers divide field CA1 pyramidal neurons into multiple subtypes with characteristic laminar distributions. And third, subcortical brain regions receiving axonal projections from molecularly distinct spatial domains of field CA1 display distinct global gene expression patterns, suggesting that field CA1 spatial domains may be genetically wired independently to form distinct functional networks related to cognition and emotion. Insights emerging from this genomic–anatomic approach provide a starting point for a detailed analysis of differential hippocampal structure–function organization.
Evidence for food storage and predomestication granaries 11,000 years ago in the Jordan Valley
Authors: Kuijt Ian , Finlayson Bill
Published: June 2009

Food storage is a vital component in the economic and social package that comprises the Neolithic, contributing to plant domestication, increasingly sedentary lifestyles, and new social organizations. Recent excavations at Dhra′ near the Dead Sea in Jordan provide strong evidence for sophisticated, purpose-built granaries in a predomestication context ≈11,300–11,175 cal B.P., which support recent arguments for the deliberate cultivation of wild cereals at this time. Designed with suspended floors for air circulation and protection from rodents, they are located between residential structures that contain plant-processing instillations. The granaries represent a critical evolutionary shift in the relationship between people and plant foods, which precedes the emergence of domestication and large-scale sedentary communities by at least 1,000 years.
SirT1 knockdown in liver decreases basal hepatic glucose production and increases hepatic insulin responsiveness in diabetic rats
Authors: Erion Derek M. , Yonemitsu Shin , Nie Yongzhan , Nagai Yoshio , Gillum Matthew P. , Hsiao Jennifer J. , Iwasaki Takanori , Stark Romana , Weismann Dirk , Yu Xing Xian , Murray Susan F. , Bhanot Sanjay , Monia Brett P. , Horvath Tamas L. , Gao Qian , Samuel Varman T. , Shulman Gerald I.
Published: June 2009

Hepatic gluconeogenesis is a major contributing factor to hyperglycemia in the fasting and postprandial states in type 2 diabetes mellitus (T2DM). Because Sirtuin 1 (SirT1) induces hepatic gluconeogenesis during fasting through the induction of phosphoenolpyruvate carboxylase kinase (PEPCK), fructose-1,6-bisphosphatase (FBPase), and glucose-6-phosphatase (G6Pase) gene transcription, we hypothesized that reducing SirT1, by using an antisense oligonucleotide (ASO), would decrease fasting hyperglycemia in a rat model of T2DM. SirT1 ASO lowered both fasting glucose concentration and hepatic glucose production in the T2DM rat model. Whole body insulin sensitivity was also increased in the SirT1 ASO treated rats as reflected by a 25% increase in the glucose infusion rate required to maintain euglycemia during the hyperinsulinemic-euglycemic clamp and could entirely be attributed to increased suppression of hepatic glucose production by insulin. The reduction in basal and clamped rates of glucose production could in turn be attributed to decreased expression of PEPCK, FBPase, and G6Pase due to increased acetylation of signal transducer and activator of transcription 3 (STAT3), forkhead box O1 (FOXO1), and peroxisome proliferator-activated receptor-γ coactivator 1α (PGC-1α), known substrates of SirT1. In addition to the effects on glucose metabolism, SirT1 ASO decreased plasma total cholesterol, which was attributed to increased cholesterol uptake and export from the liver. These results indicate that inhibition of hepatic SirT1 may be an attractive approach for treatment of T2DM.
Evidence for electronic gap-driven metal-semiconductor transition in phase-change materials
Authors: Shakhvorostov Dmitry , Nistor Razvan A. , Krusin-Elbaum Lia , Martyna Glenn J. , Newns Dennis M. , Elmegreen Bruce G. , Liu Xiao-hu , Hughes Zak E. , Paul Sujata , Cabral Cyril , Raoux Simone , Shrekenhamer David B. , Basov Dimitri N. , Song Young , Müser Martin H.
Published: June 2009

Phase-change materials are functionally important materials that can be thermally interconverted between metallic (crystalline) and semiconducting (amorphous) phases on a very short time scale. Although the interconversion appears to involve a change in local atomic coordination numbers, the electronic basis for this process is still unclear. Here, we demonstrate that in a nearly vacancy-free binary GeSb system where we can drive the phase change both thermally and, as we discover, by pressure, the transformation into the amorphous phase is electronic in origin. Correlations between conductivity, total system energy, and local atomic coordination revealed by experiments and long time ab initio simulations show that the structural reorganization into the amorphous state is driven by opening of an energy gap in the electronic density of states. The electronic driving force behind the phase change has the potential to change the interconversion paradigm in this material class.
Connexin expression by radial glia-like cells is required for neurogenesis in the adult dentate gyrus
Authors: Kunze Albrecht , Congreso Marga Rubenecia , Hartmann Christian , Wallraff-Beck Anke , Hüttmann Kerstin , Bedner Peter , Requardt Robert , Seifert Gerald , Redecker Christoph , Willecke Klaus , Hofmann Andreas , Pfeifer Alexander , Theis Martin , Steinhäuser Christian
Published: June 2009

In the adult dentate gyrus, radial glia-like cells represent putative stem cells generating neurons and glial cells. Here, we combined patch-clamp recordings, biocytin filling, immunohistochemistry, single-cell transcript analysis, and mouse transgenics to test for connexin expression and gap junctional coupling of radial glia-like cells and its impact on neurogenesis. Radial glia-like cells were identified in mice expressing EGFP under control of the
nestin
and
gfap
promoters. We show that a majority of Radial glia-like cells are coupled and express Cx43. Neuronal precursors were not coupled. Mice lacking Cx30 and Cx43 in GFAP-positive cells displayed almost complete inhibition of proliferation and a significant decline in numbers of radial glia-like cells and granule neurons. Inducible virus-mediated ablation of connexins in the adult hippocampus also reduced neurogenesis. These findings strongly suggest the requirement of connexin expression by radial glia-like cells for intact neurogenesis in the adult brain and point to possible communication pathways of these cells.
Paleocene emergence of elephant relatives and the rapid radiation of African ungulates
Authors: Gheerbrant Emmanuel
Published: June 2009

Elephants are the only living representatives of the Proboscidea, a formerly diverse mammalian order whose history began with the 55-million years (mys) oldPhosphatherium. Reported here is the discovery from the early late Paleocene of Morocco,ca.60 mys, of the oldest and most primitive elephant relative,Eritherium azzouzorumn.g., n.sp., which is one of the earliest known representatives of modern placental orders. This well supported stem proboscidean is extraordinarily primitive and condylarth-like. It provides the first dental evidence of a resemblance between the proboscideans and African ungulates (paenungulates) on the one hand and the louisinines and early macroscelideans on the other.Eritheriumillustrates the origin of the elephant order at a previously unknown primitive stage among paenungulates and “ungulates.” The primitive morphology ofEritheriumsuggests a recent and rapid paenungulate radiation after the Cretaceous-Tertiary boundary, probably favoured by early endemic African paleoecosystems. At a broader scale,Eritheriumprovides a new old calibration point of the placental tree and supports an explosive placental radiation. The Ouled Abdoun basin, which yields the oldest known African placentals, is a key locality for elucidating phylogeny and early evolution of paenungulates and other related endemic African lineages.
Translocation experiments with butterflies reveal limits to enhancement of poleward populations under climate change
Authors: Pelini Shannon L. , Dzurisin Jason D. K. , Prior Kirsten M. , Williams Caroline M. , Marsico Travis D. , Sinclair Brent J. , Hellmann Jessica J.
Published: June 2009

There is a pressing need to predict how species will change their geographic ranges under climate change. Projections typically assume that temperature is a primary fitness determinant and that populations near the poleward (and upward) range boundary are preadapted to warming. Thus, poleward, peripheral populations will increase with warming, and these increases facilitate poleward range expansions. We tested the assumption that poleward, peripheral populations are enhanced by warming using 2 butterflies (Erynnis propertiusandPapilio zelicaon) that co-occur and have contrasting degrees of host specialization and interpopulation genetic differentiation. We performed a reciprocal translocation experiment between central and poleward, peripheral populations in the field and simulated a translocation experiment that included alternate host plants. We found that the performance of both central and peripheral populations ofE. propertiuswere enhanced during the summer months by temperatures characteristic of the range center but that local adaptation of peripheral populations to winter conditions near the range edge could counteract that enhancement. Further, poleward range expansion in this species is prevented by a lack of host plants. InP. zelicaon, the fitness of central and peripheral populations decreased under extreme summer temperatures that occurred in the field at the range center. Performance in this species also was affected by an interaction of temperature and host plant such that host species strongly mediated the fitness of peripheral individuals under differing simulated temperatures. Altogether we have evidence that facilitation of poleward range shifts through enhancement of peripheral populations is unlikely in either study species.
The building blocks of economic complexity
Authors: Hidalgo César A. , Hausmann Ricardo
Published: June 2009

For Adam Smith, wealth was related to the division of labor. As people and firms specialize in different activities, economic efficiency increases, suggesting that development is associated with an increase in the number of individual activities and with the complexity that emerges from the interactions between them. Here we develop a view of economic growth and development that gives a central role to the complexity of a country's economy by interpreting trade data as a bipartite network in which countries are connected to the products they export, and show that it is possible to quantify the complexity of a country's economy by characterizing the structure of this network. Furthermore, we show that the measures of complexity we derive are correlated with a country's level of income, and that deviations from this relationship are predictive of future growth. This suggests that countries tend to converge to the level of income dictated by the complexity of their productive structures, indicating that development efforts should focus on generating the conditions that would allow complexity to emerge to generate sustained growth and prosperity.
Optical measurement of mGluR1 conformational changes reveals fast activation, slow deactivation, and sensitization
Authors: Marcaggi Païkan , Mutoh Hiroki , Dimitrov Dimitar , Beato Marco , Knöpfel Thomas
Published: June 2009

Metabotropic glutamate receptor (mGluR) activation has been extensively studied under steady-state conditions. However, at central synapses, mGluRs are exposed to brief submillisecond glutamate transients and may not reach steady-state. The lack of information on the kinetics of mGluR activation impairs accurate predictions of their operation during synaptic transmission. Here, we report experiments designed to investigate mGluR kinetics in real-time. We inserted either CFP or YFP into the second intracellular loop of mGluR1β. When these constructs were coexpressed in PC12 cells, glutamate application induced a conformational change that could be monitored, using fluorescence resonance energy transfer (FRET), with an EC
50
of 7.5 μM. The FRET response was mimicked by the agonist DHPG, abolished by the competitive antagonist MCPG, and partially inhibited by mGluR1-selective allosteric modulators. These results suggest that the FRET response reports active conformations of mGluR1 dimers. The solution exchange at the cell membrane was optimized for voltage-clamped cells by recording the current induced by co-application of 30 mM potassium. When glutamate was applied at increasing concentrations up to 2 mM, the activation time course decreased to a minimum of approximately 10 ms, whereas the deactivation time course remained constant (∼50 ms). During long-lasting applications, no desensitization was observed. In contrast, we observed a robust sensitization of the FRET response that developed over approximately 400 ms. Activation, deactivation, and sensitization time courses and amplitudes were used to derive a kinetic scheme and rate constants, from which we inferred the EC
50
and frequency dependence of mGluR1 activation under non-steady-state conditions, as occurs during synaptic transmission.
Using adult mosquitoes to transfer insecticides to
Aedes aegypti
larval habitats
Authors: Devine Gregor J. , Perea Elvira Zamora , Killeen Gerry F. , Stancil Jeffrey D. , Clark Suzanne J. , Morrison Amy C.
Published: June 2009

Vector control is a key means of combating mosquito-borne diseases and the only tool available for tackling the transmission of dengue, a disease for which no vaccine, prophylaxis, or therapeutant currently exists. The most effective mosquito control methods include a variety of insecticidal tools that target adults or juveniles. Their successful implementation depends on impacting the largest proportion of the vector population possible. We demonstrate a control strategy that dramatically improves the efficiency with which high coverage of aquatic mosquito habitats can be achieved. The method exploits adult mosquitoes as vehicles of insecticide transfer by harnessing their fundamental behaviors to disseminate a juvenile hormone analogue (JHA) between resting and oviposition sites. A series of field trials undertaken in an Amazon city (Iquitos, Peru) showed that the placement of JHA dissemination stations in just 3–5% of the available resting area resulted in almost complete coverage of sentinel aquatic habitats. More than control mortality occurred in 95–100% of the larval cohorts of
Aedes aegypti
developing at those sites. Overall reductions in adult emergence of 42–98% were achieved during the trials. A deterministic simulation model predicts amplifications in coverage consistent with our observations and highlights the importance of the residual activity of the insecticide for this technique.
Controlling transgene expression in subcutaneous implants using a skin lotion containing the apple metabolite phloretin
Authors: Gitzinger Marc , Kemmer Christian , El-Baba Marie Daoud , Weber Wilfried , Fussenegger Martin
Published: June 2009

Adjustable control of therapeutic transgenes in engineered cell implants after transdermal and topical delivery of nontoxic trigger molecules would increase convenience, patient compliance, and elimination of hepatic first-pass effect in future therapies.Pseudomonas putidaDOT-T1E has evolved the flavonoid-triggered TtgR operon, which controls expression of a multisubstrate-specific efflux pump (TtgABC) to resist plant-derived defense metabolites in its rhizosphere habitat. Taking advantage of the TtgR operon, we have engineered a hybridP. putida–mammalian genetic unit responsive to phloretin. This flavonoid is contained in apples, and, as such, or as dietary supplement, regularly consumed by humans. The engineered mammalian phloretin-adjustable control element (PEACE) enabled adjustable and reversible transgene expression in different mammalian cell lines and primary cells. Due to the short half-life of phloretin in culture, PEACE could also be used to program expression of difficult-to-produce protein therapeutics during standard bioreactor operation. When formulated in skin lotions and applied to the skin of mice harboring transgenic cell implants, phloretin was able to fine-tune target genes and adjust heterologous protein levels in the bloodstream of treated mice. PEACE-controlled target gene expression could foster advances in biopharmaceutical manufacturing as well as gene- and cell-based therapies.
An integrated genome screen identifies the Wnt signaling pathway as a major target of WT1
Authors: Kim Marianne K.-H. , McGarry Thomas J. , Ó Broin Pilib , Flatow Jared M. , Golden Aaron A.-J. , Licht Jonathan D.
Published: June 2009

WT1, a critical regulator of kidney development, is a tumor suppressor for nephroblastoma but in some contexts functions as an oncogene. A limited number of direct transcriptional targets of WT1 have been identified to explain its complex roles in tumorigenesis and organogenesis. In this study we performed genome-wide screening for direct WT1 targets, using a combination of ChIP–ChIP and expression arrays. Promoter regions bound by WT1 were highly G-rich and resembled the sites for a number of other widely expressed transcription factors such as SP1, MAZ, and ZNF219. Genes directly regulated by WT1 were implicated in MAPK signaling, axon guidance, and Wnt pathways. Among directly bound and regulated genes by WT1, nine were identified in the Wnt signaling pathway, suggesting that WT1 modulates a subset of Wnt components and responsive genes by direct binding. To prove the biological importance of the interplay between WT1 and Wnt signaling, we showed that WT1 blocked the ability of Wnt8 to induce a secondary body axis during
Xenopus
embryonic development. WT1 inhibited TCF-mediated transcription activated by Wnt ligand, wild type and mutant, stabilized β-catenin by preventing TCF4 loading onto a promoter. This was neither due to direct binding of WT1 to the TCF binding site nor to interaction between WT1 and TCF4, but by competition of WT1 and TCF4 for CBP. WT1 interference with Wnt signaling represents an important mode of its action relevant to the suppression of tumor growth and guidance of development.
Solution structure of the silkworm βGRP/GNBP3 N-terminal domain reveals the mechanism for β-1,3-glucan-specific recognition
Authors: Takahasi Kiyohiro , Ochiai Masanori , Horiuchi Masataka , Kumeta Hiroyuki , Ogura Kenji , Ashida Masaaki , Inagaki Fuyuhiko
Published: June 2009

The β-1,3-glucan recognition protein (βGRP)/Gram-negative bacteria-binding protein 3 (GNBP3) is a crucial pattern-recognition receptor that specifically binds β-1,3-glucan, a component of fungal cell walls. It evokes innate immunity against fungi through activation of the prophenoloxidase (proPO) cascade and Toll pathway in invertebrates. The βGRP consists of an N-terminal β-1,3-glucan-recognition domain and a C-terminal glucanase-like domain, with the former reported to be responsible for the proPO cascade activation. This report shows the solution structure of the N-terminal β-1,3-glucan recognition domain of silkworm βGRP. Although the N-terminal domain of βGRP has a β-sandwich fold, often seen in carbohydrate-binding modules, both NMR titration experiments and mutational analysis showed that βGRP has a binding mechanism which is distinct from those observed in previously reported carbohydarate-binding domains. Our results suggest that βGRP is a β-1,3-glucan-recognition protein that specifically recognizes a triple-helical structure of β-1,3-glucan.
Protein-free small nuclear RNAs catalyze a two-step splicing reaction
Authors: Valadkhan Saba , Mohammadi Afshin , Jaladat Yasaman , Geisler Sarah
Published: June 2009

Pre-mRNA splicing is a crucial step in eukaryotic gene expression and is carried out by a highly complex ribonucleoprotein assembly, the spliceosome. Many fundamental aspects of spliceosomal function, including the identity of catalytic domains, remain unknown. We show that a base-paired complex of U6 and U2 small nuclear RNAs, in the absence of the ≈200 other spliceosomal components, performs a two-step reaction with two short RNA oligonucleotides as substrates that results in the formation of a linear RNA product containing portions of both oligonucleotides. This reaction, which is chemically identical to splicing, is dependent on and occurs in proximity of sequences known to be critical for splicing
in vivo.
These results prove that the complex formed by U6 and U2 RNAs is a ribozyme and can potentially carry out RNA-based catalysis in the spliceosome.
The Mo-Se active site of nicotinate dehydrogenase
Authors: Wagener Nadine , Pierik Antonio J. , Ibdah Abdellatif , Hille Russ , Dobbek Holger
Published: June 2009

Nicotinate dehydrogenase (NDH) from
Eubacterium barkeri
is a molybdoenzyme catalyzing the hydroxylation of nicotinate to 6-hydroxynicotinate. Reactivity of NDH critically depends on the presence of labile (nonselenocysteine) selenium with an as-yet-unidentified form and function. We have determined the crystal structure of NDH and analyzed its active site by multiple wavelengths anomalous dispersion methods. We show that selenium is bound as a terminal Mo

Se ligand to molybdenum and that it occupies the position of the terminal sulfido ligand in other molybdenum hydroxylases. The role of selenium in catalysis has been assessed by model calculations, which indicate an acceleration of the critical hydride transfer from the substrate to the selenido ligand in the course of substrate hydroxylation when compared with an active site containing a sulfido ligand. The MoO(OH)Se active site of NDH shows a novel type of utilization and reactivity of selenium in nature.
DNA wrapping is required for DNA damage recognition in the Escherichia coli DNA nucleotide excision repair pathway
Authors: Wang Hailin , Lu Meiling , Tang Moon-shong , Van Houten Bennett , Ross J. B. Alexander , Weinfeld Michael , Le X. Chris
Published: June 2009

Localized DNA melting may provide a general strategy for recognition of the wide array of chemically and structurally diverse DNA lesions repaired by the nucleotide excision repair (NER) pathway. However, it is not clear what causes such DNA melting and how it is driven. Here, we show a DNA wrapping–melting model supported by results from dynamic monitoring of the key DNA–protein and protein–protein interactions involved in the early stages of the
Escherichia coli
NER process. Using an analytical technique involving capillary electrophoresis coupled with laser-induced fluorescence polarization, which combines a mobility shift assay with conformational analysis, we demonstrate that DNA wrapping around UvrB, mediated by UvrA, is an early event in the damage-recognition process during
E. coli
NER. DNA wrapping of UvrB was confirmed by Förster resonance energy transfer and fluorescence lifetime measurements. This wrapping did not occur with readily denaturable damaged DNA substrates (“bubble” DNA), suggesting that DNA wrapping of UvrB plays an important role in the induction of DNA melting around the damage site. Analysis of DNA wrapping of mutant UvrB Y96A further suggests that a cooperative interaction between DNA wrapping of UvrA
2
B and contact of the β-hairpin of UvrB with the bulky damage moiety may be involved in the local DNA melting at the damage site.
Regulation of myocardial ketone body metabolism by the gut microbiota during nutrient deprivation
Authors: Crawford Peter A. , Crowley Jan R. , Sambandam Nandakumar , Muegge Brian D. , Costello Elizabeth K. , Hamady Micah , Knight Rob , Gordon Jeffrey I.
Published: June 2009

Studies in mice indicate that the gut microbiota promotes energy harvest and storage from components of the diet when these components are plentiful. Here we examine how the microbiota shapes host metabolic and physiologic adaptations to periods of nutrient deprivation. Germ-free (GF) mice and mice who had received a gut microbiota transplant from conventionally raised donors were compared in the fed and fasted states by using functional genomic, biochemical, and physiologic assays. A 24-h fast produces a marked change in gut microbial ecology. Short-chain fatty acids generated from microbial fermentation of available glycans are maintained at higher levels compared with GF controls. During fasting, a microbiota-dependent, Pparα-regulated increase in hepatic ketogenesis occurs, and myocardial metabolism is directed to ketone body utilization. Analyses of heart rate, hydraulic work, and output, mitochondrial morphology, number, and respiration, plus ketone body, fatty acid, and glucose oxidation in isolated perfused working hearts from GF and colonized animals (combined with in vivo assessments of myocardial physiology) revealed that the fasted GF heart is able to sustain its performance by increasing glucose utilization, but heart weight, measured echocardiographically or as wet mass and normalized to tibial length or lean body weight, is significantly reduced in both fasted and fed mice. This myocardial-mass phenotype is completely reversed in GF mice by consumption of a ketogenic diet. Together, these results illustrate benefits provided by the gut microbiota during periods of nutrient deprivation, and emphasize the importance of further exploring the relationship between gut microbes and cardiovascular health.
Global potential for wind-generated electricity
Authors: Lu Xi , McElroy Michael B. , Kiviluoma Juha
Published: June 2009

The potential of wind power as a global source of electricity is assessed by using winds derived through assimilation of data from a variety of meteorological sources. The analysis indicates that a network of land-based 2.5-megawatt (MW) turbines restricted to nonforested, ice-free, nonurban areas operating at as little as 20% of their rated capacity could supply >40 times current worldwide consumption of electricity, >5 times total global use of energy in all forms. Resources in the contiguous United States, specifically in the central plain states, could accommodate as much as 16 times total current demand for electricity in the United States. Estimates are given also for quantities of electricity that could be obtained by using a network of 3.6-MW turbines deployed in ocean waters with depths <200 m within 50 nautical miles (92.6 km) of closest coastlines.
Engineering crystals of dendritic molecules
Authors: Lukin Oleg , Schubert Dirk , Müller Claudia M. , Schweizer W. Bernd , Gramlich Volker , Schneider Julian , Dolgonos Grygoriy , Shivanyuk Alexander
Published: June 2009

A detailed single-crystal X-ray study of conformationally flexible sulfonimide-based dendritic molecules with systematically varied molecular architectures was undertaken. Thirteen crystal structures reported in this work include 9 structures of the second-generation dendritic sulfonimides decorated with different aryl groups, 2 compounds bearing branches of both second and first generation, and 2 representatives of the first generation. Analysis of the packing patterns of 9 compounds bearing second-generation branches shows that despite their lack of strong directive functional groups there is a repeatedly reproduced intermolecular interaction mode consisting in an anchor-type packing of complementary second-generation branches of neighbouring molecules. The observed interaction tolerates a wide range of substituents inmeta- andpara-positions of the peripheral arylsulfonyl rings. Quantum chemical calculations of the molecule-molecule interaction energies agree at the qualitative level with the packing preferences found in the crystalline state. The calculations can therefore be used as a tool to rationalize and predict molecular structures with commensurate and non-commensurate branches for programming of different packing modes in crystal.
A multiscale model linking ion-channel molecular dynamics and electrostatics to the cardiac action potential
Authors: Silva Jonathan R. , Pan Hua , Wu Dick , Nekouzadeh Ali , Decker Keith F. , Cui Jianmin , Baker Nathan A. , Sept David , Rudy Yoram
Published: June 2009

Ion-channel function is determined by its gating movement. Yet, molecular dynamics and electrophysiological simulations were never combined to link molecular structure to function. We performed multiscale molecular dynamics and continuum electrostatics calculations to simulate a cardiac K
+
channel (I
Ks
) gating and its alteration by mutations that cause arrhythmias and sudden death. An all-atom model of the I
Ks
α-subunit KCNQ1, based on the recent Kv1.2 structure, is used to calculate electrostatic energies during gating. Simulations are compared with experiments where varying degrees of positive charge—added via point mutation—progressively reduce current. Whole-cell simulations show that mutations cause action potential and ECG QT interval prolongation, consistent with clinical phenotypes. This framework allows integration of multiscale observations to study the molecular basis of excitation and its alteration by disease.
Amino acid polymorphisms altering the glycosylation of IL-2 do not protect from type 1 diabetes in the NOD mouse
Authors: Kamanaka Masahito , Rainbow Dan , Schuster-Gossler Karin , Eynon Elizabeth E. , Chervonsky Alexander V. , Wicker Linda S. , Flavell Richard A.
Published: June 2009

Idd3is one of many gene regions that affect the development of type 1 diabetes (T1D) in the nonobese diabetic (NOD) mouse.Idd3has been localized to a 650-kb region on chromosome 3 containing the IL-2 gene. Exon 1 of the IL-2 gene is polymorphic between the susceptible NOD and the protective C57BL/6 (B6) alleles, causing multiple amino acid changes that have been proposed to be responsible for the differing glycosylation status. To address whether this coding polymorphism recapitulates the disease suppression mediated by the B6Idd3allele, we generated knockin mice in which exon 1 of the B6 IL-2 allele replaces the homologous region in the NOD allele. We generated these mice by targeting the NOD allele of NOD/129 F1ES cells. IL-2 protein from the knockin mice showed the glycosylation pattern of the B6 IL-2 isoform, confirming that the amino acid differences encoded within exon 1 affect the glycosylation of the IL-2 protein. However, unlike NOD.B6Idd3congenic mice, the knockin mice were not protected from T1D. Furthermore, the difference in amino acid sequence in the IL-2 protein did not affect the level of expression of IL-2. This approach provides a general method for the determination of a functional role of a given genomic sequence in a disease process. Further, our result demonstrates that the variants in exon 1 of the IL-2 gene are not responsible for T1D suppression in NOD.B6 Idd3 mice, thereby supporting the hypothesis that variants in the regulatory region affecting expression levels are causative.
Improved spatial learning performance of fat-1 mice is associated with enhanced neurogenesis and neuritogenesis by docosahexaenoic acid
Authors: He Chengwei , Qu Xiying , Cui Libin , Wang Jingdong , Kang Jing X.
Published: June 2009

Docosahexaenoic acid (DHA), an n-3 long chain polyunsaturated fatty acid (LC-PUFA), highly enriched in the central nervous system, is critical for brain development and function. It has been shown that DHA deficiency impairs cognitive performance whereas DHA supplementation improves the condition. However, the mechanisms underlying the role of DHA in brain development and function remain to be elucidated. By using transgenic fat-1 mice rich in endogenous n-3 PUFA, we show that increased brain DHA significantly enhances hippocampal neurogenesis shown by an increased number of proliferating neurons and neuritogenesis, evidenced by increased density of dendritic spines of CA1 pyramidal neurons in the hippocampus. Concurrently, fat-1 mice exhibit a better spatial learning performance in the Morris water maze compared with control WT littermates. In vitro experiments further demonstrate that DHA promotes differentiation and neurite outgrowth of neuronal cells derived from mouse ES cells and increases the proliferation of cells undergoing differentiation into neuronal lineages from the ES cells. These results together provide direct evidence for a promoting effect of DHA on neurogenesis and neuritogenesis and suggest that this effect may be a mechanism underlying its beneficial effect on behavioral performance.
Modeling the immune rheostat of macrophages in the lung in response to infection
Authors: Day Judy , Friedman Avner , Schlesinger Larry S.
Published: June 2009

In the lung, alternatively activated macrophages (AAM) form the first line of defense against microbial infection. Due to the highly regulated nature of AAM, the lung can be considered as an immunosuppressive organ for respiratory pathogens. However, as infection progresses in the lung, another population of macrophages, known as classically activated macrophages (CAM) enters; these cells are typically activated by IFN-γ. CAM are far more effective than AAM in clearing the microbial load, producing proinflammatory cytokines and antimicrobial defense mechanisms necessary to mount an adequate immune response. Here, we are concerned with determining the first time when the population of CAM becomes more dominant than the population of AAM. This proposed “switching time” is explored in the context ofMycobacterium tuberculosis(MTb) infection. We have developed a mathematical model that describes the interactions among cells, bacteria, and cytokines involved in the activation of both AAM and CAM. The model, based on a system of differential equations, represents a useful tool to analyze strategies for reducing the switching time, and to generate hypotheses for experimental testing.
An engineered substance P variant for receptor-mediated delivery of synthetic antibodies into tumor cells
Authors: Rizk Shahir S. , Luchniak Anna , Uysal Serdar , Brawley Crista M. , Rock Ronald S. , Kossiakoff Anthony A.
Published: June 2009

We have developed and tested a robust delivery method for the transport of proteins to the cytoplasm of mammalian cells without compromising the integrity of the cell membrane. This receptor-mediated delivery (RMD) technology utilizes a variant of substance P (SP), a neuropeptide that is rapidly internalized upon interaction with the neurokinin-1 receptor (NK1R). Cargos in the form of synthetic antibody fragments (sABs) were conjugated to the engineered SP variant (SPv) and efficiently internalized by NK1R-expressing cells. The sABs used here were generated to bind specific conformational forms of actin. The internalized proteins appear to escape the endosome and retain their binding activity within the cells as demonstrated by co-localization with the actin cytoskeleton. Further, since the NK1R is over-expressed in many cancers, SPv-mediated delivery provides a highly specific method for therapeutic utilization of affinity reagents targeting intracellular processes in diseased tissue.
Eukaryotic cytosolic and mitochondrial phenylalanyl-tRNA synthetases catalyze the charging of tRNA with the
meta
-tyrosine
Authors: Klipcan Liron , Moor Nina , Kessler Naama , Safro Mark G.
Published: June 2009

The accumulation of proteins damaged by reactive oxygen species (ROS), conventionally regarded as having pathological potentials, is associated with age-related diseases such as Alzheimer's, atherosclerosis, and cataractogenesis. Exposure of the aromatic amino acid phenylalanine to ROS-generating systems produces multiple isomers of tyrosine:
m
-tyrosine (
m
-Tyr),
o
-tyrosine (
o
-Tyr), and the standard
p
-tyrosine (Tyr). Previously it was demonstrated that exogenously supplied, oxidized amino acids could be incorporated into bacterial and eukaryotic proteins. It is, therefore, likely that in many cases, in vivo-damaged amino acids are available for de novo synthesis of proteins. Although the involvement of aminoacyl-tRNA synthetases in this process has been hypothesized, the specific pathway by which ROS-damaged amino acids are incorporated into proteins remains unclear. We provide herein evidence that mitochondrial and cytoplasmic phenylalanyl-tRNA synthetases (
Hsmt
PheRS and
Hsct
PheRS, respectively) catalyze direct attachment of
m
-Tyr to tRNA
Phe
, thereby opening the way for delivery of the misacylated tRNA to the ribosome and incorporation of ROS-damaged amino acid into eukaryotic proteins. Crystal complexes of mitochondrial and bacterial PheRSs with
m
-Tyr reveal the net of highly specific interactions within the synthetic and editing sites.
TARP modulation of synaptic AMPA receptor trafficking and gating depends on multiple intracellular domains
Authors: Milstein Aaron D. , Nicoll Roger A.
Published: June 2009

Previous work has established stargazin and its related family of transmembrane AMPA receptor regulatory proteins (TARPs) as auxiliary subunits of AMPA receptors (AMPARs) that control synaptic strength both by targeting AMPARs to synapses through an intracellular PDZ-binding motif and by modulating their gating through an extracellular domain. However, TARPs γ-2 and γ-8 differentially regulate the synaptic targeting of AMPARs, despite having identical PDZ-binding motifs. Here, we investigate the structural elements that contribute to this functional difference between TARP subtypes by using domain transplantation and truncation. We identify a component of synaptic AMPAR trafficking that is independent of the TARP C-terminal PDZ-binding motif, and we establish previously uncharacterized roles for the TARP intracellular N terminus, loop, and C terminus in modulating both the trafficking and gating of synaptic AMPARs.
Cryopreserved blastocysts have a lower implantation but an equal live birth rate as compared to fresh blastocysts of the same quality – a case–control study
Authors: SHEBL OMAR , EBNER THOMAS , SOMMERGRUBER MICHAEL , SIR ANDREAS , TEWS GERNOT
Published: June 2009

The purpose of this case–control study was to compare implantation, pregnancy, and live birth rate of cryopreserved embryos with that of fresh embryos. A total of 1,488 assisted reproductive technology (ART) trials including 188 cryopreserved embryo replacement trials were reviewed. After proofing the exclusion criteria, 112 patients undergoing a cryopreserved embryo replacement (study group) were matched with 112 patients undergoing a fresh embryo transfer (control group). Matching was done for age of patients, number, and quality of embryos (Day 5 embryos). Data concerning maternal characteristics, survival rate of warming procedure, implantation, pregnancy, ongoing pregnancy, and live birth rates were collected. A lower implantation rate was found for cryopreserved embryo replacement compared to transferring fresh embryos. Live birth rate was found to be equal in both groups.
Desmoglein 1–dependent suppression of EGFR signaling promotes epidermal differentiation and morphogenesis
Authors: Getsios Spiro , Simpson Cory L. , Kojima Shin-ichiro , Harmon Robert , Sheu Linda J. , Dusek Rachel L. , Cornwell Mona , Green Kathleen J.
Published: June 2009

Dsg1 (desmoglein 1) is a member of the cadherin family of Ca2+-dependent cell adhesion molecules that is first expressed in the epidermis as keratinocytes transit out of the basal layer and becomes concentrated in the uppermost cell layers of this stratified epithelium. In this study, we show that Dsg1 is not only required for maintaining epidermal tissue integrity in the superficial layers but also supports keratinocyte differentiation and suprabasal morphogenesis. Dsg1 lacking N-terminal ectodomain residues required for adhesion remained capable of promoting keratinocyte differentiation. Moreover, this capability did not depend on cytodomain interactions with the armadillo protein plakoglobin or coexpression of its companion suprabasal cadherin, Dsc1 (desmocollin 1). Instead, Dsg1 was required for suppression of epidermal growth factor receptor–Erk1/2 (extracellular signal-regulated kinase 1/2) signaling, thereby facilitating keratinocyte progression through a terminal differentiation program. In addition to serving as a rigid anchor between adjacent cells, this study implicates desmosomal cadherins as key components of a signaling axis governing epithelial morphogenesis.
Microcephalin and pericentrin regulate mitotic entry via centrosome-associated Chk1
Authors: Tibelius Alexandra , Marhold Joachim , Zentgraf Hanswalter , Heilig Christoph E. , Neitzel Heidemarie , Ducommun Bernard , Rauch Anita , Ho Anthony D. , Bartek Jiri , Krämer Alwin
Published: June 2009

Primary microcephaly, Seckel syndrome, and microcephalic osteodysplastic primordial dwarfism type II (MOPD II) are disorders exhibiting marked microcephaly, with small brain sizes reflecting reduced neuron production during fetal life. Although primary microcephaly can be caused by mutations in microcephalin (MCPH1), cells from patients with Seckel syndrome and MOPD II harbor mutations in ataxia telangiectasia and Rad3 related (ATR) or pericentrin (PCNT), leading to disturbed ATR signaling. In this study, we show that a lack of MCPH1 or PCNT results in a loss of Chk1 from centrosomes with subsequently deregulated activation of centrosomal cyclin B–Cdk1.
The Drosophila deoxyhypusine hydroxylase homologue nero and its target eIF5A are required for cell growth and the regulation of autophagy
Authors: Patel Prajal H. , Costa-Mattioli Mauro , Schulze Karen L. , Bellen Hugo J.
Published: June 2009

Hypusination is a unique posttranslational modification by which lysine is transformed into the atypical amino acid hypusine. eIF5A (eukaryotic initiation factor 5A) is the only known protein to contain hypusine. In this study, we describe the identification and characterization of nero, the Drosophila melanogaster deoxyhypusine hydroxylase (DOHH) homologue. nero mutations affect cell and organ size, bromodeoxyuridine incorporation, and autophagy. Knockdown of the hypusination target eIF5A via RNA interference causes phenotypes similar to nero mutations. However, loss of nero appears to cause milder phenotypes than loss of eIF5A. This is partially explained through a potential compensatory mechanism by which nero mutant cells up-regulate eIF5A levels. The failure of eIF5A up-regulation to rescue nero mutant phenotypes suggests that hypusination is required for eIF5A function. Furthermore, expression of enzymatically impaired forms of DOHH fails to rescue nero clones, indicating that hypusination activity is important for nero function. Our data also indicate that nero and eIF5A are required for cell growth and affect autophagy and protein synthesis.
Cytokine-dependent regulation of NADPH oxidase activity and the consequences for activated T cell homeostasis
Authors: Purushothaman Divya , Sarin Apurva
Published: June 2009

Cellular dependence on growth factors for survival is developmentally programmed and continues in adult metazoans. Antigen-activated T cell apoptosis in the waning phase of the immune response is thought to be triggered by depletion of cytokines from the microenvironment. T cell apoptosis resulting from cytokine deprivation is mediated by reactive oxygen species (ROS), but their source and position in the apoptotic cascade is poorly understood. RNA interference approaches implicated the nicotinamide adenine dinucleotide phosphate (NADPH) oxidase in neglect-induced apoptosis in T cells. Using mice deficient for the catalytic subunit gp91phox to characterize the molecular link to activated T cell apoptosis, we show that gp91phox-deficient T (T−/−) cells generated mitochondrial superoxide but had diminished hydrogen peroxide production in response to neglect, which, in turn, regulated Jun N-terminal kinase–dependent Bax activation and apoptosis. Activated T−/− cells were distinguished by improved survival after activation by superantigens in vivo, adoptive transfers into congenic hosts, and higher recall responses after immunization. Thus, the NADPH oxidase may regulate adaptive immunity in addition to its previously well-characterized role in the innate response.