bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of excess Mg and nano-additives on the superconducting properties of weakly connected bulk MgB2
Authors: Bhadauria P. P. S. , Gupta Anurag , Kishan Hari , Narlikar A. V.
Published: February 2013

Series of ex-situ polycrystalline MgB2 bulk samples, by adding different additives like more of excess Mg (5 wt. %), nanoparticles of Ag (3 wt. %), and SiC (10 wt. %) to a previously optimized composition MgB2 + Mg (5 wt. %), were prepared by solid state synthesis route. Detailed investigations were carried out by XRD, SEM, and thermoelectric power S(T), resistivity ρ(T), and magnetization M(B) at temperatures T = 4.2–300 K and applied fields B = 0–8 T. All the samples typically show low connectivity (i.e., normal state current carrying cross section ∼0.9%–3%). The effect of different additives was different on the critical current density (Jc) of the samples. The Jc, for instance at T = 4.2 K and B = 1 T, varied between 4.8 × 107 and 2.8 × 108 A/m2 for various samples. In comparison to the previously optimized values, the Jc was enhanced by further addition of 5 wt. % Mg and degraded both by nano-SiC and nano-Ag addition. However, many of the other properties of the samples were not much affected. For instance, the samples did not show any change in the superconducting onsets, S(T) and the parallel upper critical field (Bc2|| (T) ∼ 11–13 T at 20 K and 20–21 T at 4.2 K). The Jc(B) dependence also shows similar behavior in all the samples, where the Jc is found to scale as B−1 up to a sample independent crossover field Bcr ∼ 2 T and 1.3 T at T = 4.2 and 20 K, respectively. At higher fields B > Bcr, the Jc(B) curves branch out and decrease rapidly towards zero at a sample dependent characteristic field. We try to understand these results quantitatively in terms of changes in connectivity, pinning, and anisotropy driven percolation. However, all our results and analysis point out that the intra-particle regions stay unaffected and mainly the inter-particle regions get affected by the additives leading to the Jc variation in the weakly connected samples.
Correlation between structural parameters and the magnetocaloric effect in epitaxial La0.8Ca0.2MnO3/LaAlO3 thin film
Authors: Debnath J. C. , Kim J. H. , Heo Y. , Strydom A. M. , Dou S. X.
Published: February 2013

An epitaxial La0.8Ca0.2MnO3/LaAlO3 (LCMO/LAO) thin film was fabricated using the pulsed laser deposition technique to evaluate the correlation between the crystal structure and the magnetocaloric effect. In our study, the LCMO film was 200 nm in thickness and appeared to have a strong out-of plane texture. We found that each column in the LCMO thin film layer is a domain which has a different ordering direction. These microscopic feature results in anisotropic properties of magnetization, entropy, and relative cooling power. The film exhibited a paramagnetic-to-ferromagnetic second order phase transition at 249 K. The lack of any hysteresis loss also confirmed that the material is intrinsically reversible. In addition, the large magnetization of the thin film results in an entropy change larger than those of all other perovskite type materials. Consequently, the relative cooling power is significantly enhanced.
Rate equation analysis of injection-locked quantum cascade lasers
Authors: Wang Cheng , Grillot Frédéric , Kovanis Vassilios , Even Jacky
Published: February 2013

The modulation properties of optical injection-locked quantum cascade lasers (QCLs) are investigated theoretically via a simple low dimensional rate equation model. It is found that both strong injection level and positive optical frequency detuning increase the modulation bandwidth, while a large linewidth enhancement factor (LEF) contributes to the enhancement of the peak magnitude in the intensity modulation (IM) response. As opposed to conventional injection-locked interband lasers, it is demonstrated that no dip occurs in the QCL's IM response, which is beneficial for a series of broadband microwave photonic applications. Computations also show that the value of the LEF can critically modify both the locking and stability regions on the optical frequency detuning injection level map.
Subwavelength superfocusing with a dipole-wave-reciprocal binary zone plate
Authors: Wang Jun , Qin Fei , Hua Zhang Dao , Li Dongdong , Wang Yueke , Shen Xiaonan , Yu Ting , Teng Jinghua
Published: February 2013

We propose an idea of using a convergent dipole wave at the aperture, radiated from a dipole at distance of z0, to produce a perfect focusing at z0. We verified this idea through simulation and experimental observation. It is demonstrated that the zone plate designed based on the idea can provide a subwavelength superfocusing by effectively bending the surface waves in a Fresnel region of 100 nm to a couple of wavelengths and is suitable for a situation where a superresolution at a micro working distance is essential.
Optimization of laser-target interaction for proton acceleration
Authors: d'Humières E. , Brantov A. , Yu. Bychenkov V. , Tikhonchuk V. T.
Published: February 2013

The aim of this study is to optimize the characteristics, in particular, the maximum energy and the number of high energy protons accelerated by a high intensity laser from different targets by using two- and three-dimensional particle-in-cell simulations. Two principal ways are considered to increase the maximum proton energy: (1) the use of an optimized target design (by choosing its atomic composition, density, structure, thickness, and transverse size); (2) variation of the laser pulse parameters (duration, power, intensity, focal spot size, polarization, pulse shape, etc.). Our analysis demonstrates a possibility to accelerate protons to the energies exceeding 200 MeV with 20 J laser pulses with appropriately chosen focusing and duration.
Viscoplastic analysis of cyclic indentation behavior of thin metallic films
Authors: Blada C. B. , Shen Y.-L.
Published: February 2013

The indentation behavior of metallic thin film is studied numerically, with attention devoted to cyclic response under a fixed load amplitude. The finite element model consists of an aluminum (Al) film above a silicon (Si) substrate, subject to indentation by a diamond indenter. The rate-dependent viscoplastic model of Al is employed. It is shown that, toward the end of the reloading phase of each cycle, plastic deformation continues to occur and the indenter moves deeper into the material. The advancing rate decreases with time, leading to a stabilized response after about ten cycles, in agreement with experimental measurement. Tracking of local deformation history is carried out, to corroborate with the macroscopic indentation response obtained from modeling and experiment.
Factors involved in high ewe losses in winter lambing flocks grazing dual-purpose wheat in southern New South Wales: a producer survey
Authors: McGrath S. R. , Lievaart J. J. , Virgona J. M. , Bhanugopan M. S. , Friend M. A.
Published: February 2013

A comparative survey was undertaken with 43 sheep producers in southern New South Wales using a semi-structured interview to investigate factors associated with high ewe mortality rates in winter lambing flocks grazing dual-purpose wheat. Participants were classified as either control (n = 23), who had not observed abnormally high ewe deaths, or case (n = 20), who had observed abnormally high ewe mortality rates when sheep grazed dual-purpose wheat. Ewe losses associated with grazing wheat were higher in the case group compared with the control group (8.6 vs 1.8%; P < 0.001) and there was also more deaths attributed to metabolic disease (3.4 vs 0.6%; P < 0.05). A higher proportion of control respondents had provided magnesium or sodium supplementation to ewes grazing wheat (P < 0.05). The body condition score of ewes entering the grazing period was significantly higher in the control group (3.2 vs 2.8; P < 0.05). The proportion of respondents who fed roughage to ewes grazing wheat did not differ significantly between control and case groups (48 vs 35%). A higher proportion of respondents in the case group had supplied grain to ewes (25 vs 0%; P < 0.05), which may have been associated with the lower body condition of sheep in these flocks compared with the control group. It was concluded that supplying ad libitum access to mineral supplements that include magnesium, sodium and possibly calcium, and maintaining adequate body condition score can reduce the risk of high ewe mortality rates when reproducing ewes graze dual-purpose wheat.
Photosynthetic rate and biochemical composition of green algae Ulva flexuosa (Wulfen) J. Agardh as potential indicators of environmental stress in the intertidal zones
Authors: Prakash R. , Jokhan A. D.
Published: February 2013

Photosynthetic rate and biochemical composition total chlorophyll (TC), total soluble protein (TSP) and total soluble carbohydrates (TSC) were determined for Ulva flexuosa, a green marine algae collected from Nasese, Lami and Laucala Beach areas in Suva, Fiji Islands. Ulva flexuosa from Laucala Beach area had the highest photosynthetic rates, TC and TSP content, while algae from Nasese area had the highest amount of TSC. Algae from Lami area had the lowest amount of photosynthesis rate, TC, TSP and TSC. High photosynthetic rate and biochemical content were mainly due to the presence of high levels of nitrogen in the area. Algae thrived in Laucala Beach and Nasese area where nitrogen content was high. Low photosynthetic rate and biochemical composition were recorded in algae from the Lami area, which was apparently the most polluted area. It appeared that conditions in Lami area were intolerable to U. flexuosa. Algae collected from the three sites differed in the measured parameters with respect to the differences in the pH, temperature and nitrogen levels indicating that physiological responses of algae could be used as indicators to monitor the environmental quality of the intertidal zones.
Positive and negative feedback loops in the p53 and mRNA 3′ processing pathways
Authors: Devany Emral , Zhang Xiaokan , Park Ji Yeon , Tian Bin , Kleiman Frida Esther
Published: February 2013

Although the p53 network has been intensively studied, genetic analyses long hinted at the existence of components that remained elusive. Recent studies have shown regulation of p53 at the mRNA level mediated via both the 5′ and the 3′ untranslated regions and affecting the stability and translation efficiency of the p53 mRNA. Here, we provide evidence of a feedback loop between p53 and the poly(A)-specific ribonuclease (PARN), in which PARN deadenylase keeps p53 levels low in nonstress conditions by destabilizing p53 mRNA, and the UV-induced increase in p53 activates PARN deadenylase, regulating gene expression during DNA damage response in a transactivation-independent manner. This model is innovative because it provides insights into p53 function and the mechanisms behind the regulation of mRNA 3′ end processing in different cellular conditions.
Meiotic HORMA domain proteins prevent untimely centriole disengagement during
Caenorhabditis elegans
spermatocyte meiosis
Authors: Schvarzstein Mara , Pattabiraman Divya , Bembenek Joshua N. , Villeneuve Anne M.
Published: February 2013

In many species where oocytes lack centrosomes, sperm contribute both genetic material and centriole(s) to the zygote. Correct centriole organization during male meiosis is critical to guarantee a normal bipolar mitotic spindle in the zygote. During
Caenorhabditis elegans
male meiosis, centrioles normally undergo two rounds of duplication, resulting in haploid sperm each containing a single tightly engaged centriole pair. Here we identify an unanticipated role for
C. elegans
HORMA (Hop1/Rev7/Mad2) domain proteins HTP-1/2 and HIM-3 in regulating centriole disengagement during spermatocyte meiosis. In
him-3
and
htp-1 htp-2
mutants, centrioles separate inappropriately during meiosis II, resulting in spermatids with disengaged centrioles. Moreover, extra centrosomes are detected in a subset of zygotes. Together, these data implicate HIM-3 and HTP-1/2 in preventing centriole disengagement during meiosis II. We showed previously that HTP-1/2 prevents premature loss of sister chromatid cohesion during the meiotic divisions by inhibiting removal of meiotic cohesin complexes containing the REC-8 subunit. Worms lacking REC-8, or expressing a mutant separase protein with elevated local concentration at centrosomes and in sperm, likewise exhibit inappropriate centriole separation during spermatocyte meiosis. These observations are consistent with HIM-3 and HTP-1/2 preventing centriole disengagement by inhibiting separase-dependent cohesin removal. Our data suggest that the same specialized meiotic mechanisms that function to prevent premature release of sister chromatid cohesion during meiosis I in
C. elegans
also function to inhibit centriole separation at meiosis II, thereby ensuring that the zygote inherits the appropriate complement of chromosomes and centrioles.
Morphology transition in lipid vesicles due to in-plane order and topological defects
Authors: Hirst Linda S. , Ossowski Adam , Fraser Matthew , Geng Jun , Selinger Jonathan V. , Selinger Robin L. B.
Published: February 2013

Complex morphologies in lipid membranes typically arise due to chemical heterogeneity, but in the tilted gel phase, complex shapes can form spontaneously even in a membrane containing only a single lipid component. We explore this phenomenon via experiments and coarse-grained simulations on giant unilamellar vesicles of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine. When cooled from the untilted L
α
liquid-crystalline phase into the

tilted gel phase, vesicles deform from smooth spheres to disordered, highly crumpled shapes. We propose that this shape evolution is driven by nucleation of complex membrane microstructure with topological defects in the tilt orientation that induce nonuniform membrane curvature. Coarse-grained simulations demonstrate this mechanism and show that kinetic competition between curvature change and defect motion can trap vesicles in deeply metastable, defect-rich structures.
Structure of an actin-related subcomplex of the SWI/SNF chromatin remodeler
Authors: Schubert Heidi L. , Wittmeyer Jacqueline , Kasten Margaret M. , Hinata Kaede , Rawling David C. , Héroux Annie , Cairns Bradley R. , Hill Christopher P.
Published: February 2013

The packaging of DNA into nucleosomal structures limits access for templated processes such as transcription and DNA repair. The repositioning or ejection of nucleosomes is therefore critically important for regulated events, including gene expression. This activity is provided by chromatin remodeling complexes, or remodelers, which are typically large, multisubunit complexes that use an ATPase subunit to translocate the DNA. Many remodelers contain pairs or multimers of actin-related proteins (ARPs) that contact the helicase-SANT–associated (HSA) domain within the catalytic ATPase subunit and are thought to regulate ATPase activity. Here, we determined the structure of a four-protein subcomplex within the SWI/SNF remodeler that comprises the Snf2 HSA domain, Arp7, Arp9, and repressor of
Ty1
transposition, gene 102 (Rtt102). Surprisingly, unlike characterized actin–actin associations, the two ARPs pack like spoons and straddle the HSA domain, which forms a 92-Å-long helix. The ARP–HSA interactions are reminiscent of contacts between actin and many binding partners and are quite different from those in the Arp2/3 complex. Rtt102 wraps around one side of the complex in a highly extended conformation that contacts both ARPs and therefore stabilizes the complex, yet functions to reduce by ∼2.4-fold the remodeling and ATPase activity of complexes containing the Snf2 ATPase domain. Thus, our structure provides a foundation for developing models of remodeler function, including mechanisms of coupling between ARPs and the ATPase translocation activity.
Improving spinning disk confocal microscopy by preventing pinhole cross-talk for intravital imaging
Authors: Shimozawa Togo , Yamagata Kazuo , Kondo Takefumi , Hayashi Shigeo , Shitamukai Atsunori , Konno Daijiro , Matsuzaki Fumio , Takayama Jun , Onami Shuichi , Nakayama Hiroshi , Kosugi Yasuhito , Watanabe Tomonobu M. , Fujita Katsumasa , Mimori-Kiyosue Yuko
Published: February 2013

A recent key requirement in life sciences is the observation of biological processes in their natural in vivo context. However, imaging techniques that allow fast imaging with higher resolution in 3D thick specimens are still limited. Spinning disk confocal microscopy using a Yokogawa Confocal Scanner Unit, which offers high-speed multipoint confocal live imaging, has been found to have wide utility among cell biologists. A conventional Confocal Scanner Unit configuration, however, is not optimized for thick specimens, for which the background noise attributed to “pinhole cross-talk,” which is unintended pinhole transmission of out-of-focus light, limits overall performance in focal discrimination and reduces confocal capability. Here, we improve spinning disk confocal microscopy by eliminating pinhole cross-talk. First, the amount of pinhole cross-talk is reduced by increasing the interpinhole distance. Second, the generation of out-of-focus light is prevented by two-photon excitation that achieves selective-plane illumination. We evaluate the effect of these modifications and test the applicability to the live imaging of green fluorescent protein-expressing model animals. As demonstrated by visualizing the fine details of the 3D cell shape and submicron-size cytoskeletal structures inside animals, these strategies dramatically improve higher-resolution intravital imaging.
Particle shape enhances specificity of antibody-displaying nanoparticles
Authors: Barua Sutapa , Yoo Jin-Wook , Kolhar Poornima , Wakankar Aditya , Gokarn Yatin R. , Mitragotri Samir
Published: February 2013

Monoclonal antibodies are used in numerous therapeutic and diagnostic applications; however, their efficacy is contingent on specificity and avidity. Here, we show that presentation of antibodies on the surface of nonspherical particles enhances antibody specificity as well as avidity toward their targets. Using spherical, rod-, and disk-shaped polystyrene nano- and microparticles and trastuzumab as the targeting antibody, we studied specific and nonspecific uptake in three breast cancer cell lines: BT-474, SK-BR-3, and MDA-MB-231. Rods exhibited higher specific uptake and lower nonspecific uptake in all cells compared with spheres. This surprising interplay between particle shape and antibodies originates from the unique role of shape in determining binding and unbinding of particles to cell surface. In addition to exhibiting higher binding and internalization, trastuzumab-coated rods also exhibited greater inhibition of BT-474 breast cancer cell growth in vitro to a level that could not be attained by soluble forms of the antibody. The effect of trastuzumab-coated rods on cells was enhanced further by replacing polystyrene particles with pure chemotherapeutic drug nanoparticles of comparable dimensions made from camptothecin. Trastuzumab-coated camptothecin nanoparticles inhibited cell growth at a dose 1,000-fold lower than that required for comparable inhibition of growth using soluble trastuzumab and 10-fold lower than that using BSA-coated camptothecin. These results open unique opportunities for particulate forms of antibodies in therapeutics and diagnostics.
Vegetation engineers marsh morphology through multiple competing stable states
Authors: Marani Marco , Da Lio Cristina , D’Alpaos Andrea
Published: February 2013

Marshes display impressive biogeomorphic features, such as zonation, a mosaic of extensive vegetation patches of rather uniform composition, exhibiting sharp transitions in the presence of extremely small topographic gradients. Although generally associated with the accretion processes necessary for marshes to keep up with relative sea level rise, competing environmental constraints, and ecologic controls, zonation is still poorly understood in terms of the underlying biogeomorphic mechanisms. Here we find, through observations and modeling interpretation, that zonation is the result of coupled geomorphological–biological dynamics and that it stems from the ability of vegetation to actively engineer the landscape by tuning soil elevation within preferential ranges of optimal adaptation. We find multiple peaks in the frequency distribution of observed topographic elevation and identify them as the signature of biologic controls on geomorphodynamics through competing stable states modulated by the interplay of inorganic and organic deposition. Interestingly, the stable biogeomorphic equilibria correspond to suboptimal rates of biomass production, a result coherent with recent observations. The emerging biogeomorphic structures may display varying degrees of robustness to changes in the rate of sea level rise and sediment availability, with implications for the overall resilience of marsh ecosystems to climatic changes.
Inhibition of the prostaglandin receptor EP2 following status epilepticus reduces delayed mortality and brain inflammation
Authors: Jiang Jianxiong , Quan Yi , Ganesh Thota , Pouliot Wendy A. , Dudek F. Edward , Dingledine Raymond
Published: February 2013

Prostaglandin E2 is now widely recognized to play critical roles in brain inflammation and injury, although the responsible prostaglandin receptors have not been fully identified. We developed a potent and selective antagonist for the prostaglandin E2 receptor subtype EP2, TG6-10-1, with a sufficient pharmacokinetic profile to be used in vivo. We found that in the mouse pilocarpine model of status epilepticus (SE), systemic administration of TG6-10-1 completely recapitulates the effects of conditional ablation of cyclooxygenase-2 from principal forebrain neurons, namely reduced delayed mortality, accelerated recovery from weight loss, reduced brain inflammation, prevention of blood–brain barrier opening, and neuroprotection in the hippocampus, without modifying seizures acutely. Prolonged SE in humans causes high mortality and morbidity that are associated with brain inflammation and injury, but currently the only effective treatment is to stop the seizures quickly enough with anticonvulsants to prevent brain damage. Our results suggest that the prostaglandin receptor EP2 is critically involved in neuroinflammation and neurodegeneration, and point to EP2 receptor antagonism as an adjunctive therapeutic strategy to treat SE.
Correlative live-cell and superresolution microscopy reveals cargo transport dynamics at microtubule intersections
Authors: Bálint Štefan , Verdeny Vilanova Ione , Sandoval Álvarez Ángel , Lakadamyali Melike
Published: February 2013

Intracellular transport plays an essential role in maintaining the organization of polarized cells. Motor proteins tether and move cargos along microtubules during long-range transport to deliver them to their proper location of function. To reach their destination, cargo-bound motors must overcome barriers to their forward motion such as intersection points between microtubules. The ability to visualize how motors navigate these barriers can give important information about the mechanisms that lead to efficient transport. Here, we first develop an all-optical correlative imaging method based on single-particle tracking and superresolution microscopy to map the transport trajectories of cargos to individual microtubules with high spatiotemporal resolution. We then use this method to study the behavior of lysosomes at microtubule–microtubule intersections. Our results show that the intersection poses a significant hindrance that leads to long pauses in transport only when the separation distance of the intersecting microtubules is smaller than ∼100 nm. However, the obstructions are typically overcome by the motors with high fidelity by either switching to the intersecting microtubule or eventually passing through the intersection. Interestingly, there is a large tendency to maintain the polarity of motion (anterograde or retrograde) after the intersection, suggesting a high degree of regulation of motor activity to maintain transport in a given direction. These results give insights into the effect of the cytoskeletal geometry on cargo transport and have important implications for the mechanisms that cargo-bound motors use to maneuver through the obstructions set up by the complex cytoskeletal network.
Engineering of a functional bone organ through endochondral ossification
Authors: Scotti Celeste , Piccinini Elia , Takizawa Hitoshi , Todorov Atanas , Bourgine Paul , Papadimitropoulos Adam , Barbero Andrea , Manz Markus G. , Martin Ivan
Published: February 2013

Embryonic development, lengthening, and repair of most bones proceed by endochondral ossification, namely through formation of a cartilage intermediate. It was previously demonstrated that adult human bone marrow-derived mesenchymal stem/stromal cells (hMSCs) can execute an endochondral program and ectopically generate mature bone. Here we hypothesized that hMSCs pushed through endochondral ossification can engineer a scaled-up ossicle with features of a “bone organ,” including physiologically remodeled bone, mature vasculature, and a fully functional hematopoietic compartment. Engineered hypertrophic cartilage required IL-1β to be efficiently remodeled into bone and bone marrow upon subcutaneous implantation. This model allowed distinguishing, by analogy with bone development and repair, an outer, cortical-like perichondral bone, generated mainly by host cells and laid over a premineralized area, and an inner, trabecular-like, endochondral bone, generated mainly by the human cells and formed over the cartilaginous template. Hypertrophic cartilage remodeling was paralleled by ingrowth of blood vessels, displaying sinusoid-like structures and stabilized by pericytic cells. Marrow cavities of the ossicles contained phenotypically defined hematopoietic stem cells and progenitor cells at similar frequencies as native bones, and marrow from ossicles reconstituted multilineage long-term hematopoiesis in lethally irradiated mice. This study, by invoking a “developmental engineering” paradigm, reports the generation by appropriately instructed hMSC of an ectopic “bone organ” with a size, structure, and functionality comparable to native bones. The work thus provides a model useful for fundamental and translational studies of bone morphogenesis and regeneration, as well as for the controlled manipulation of hematopoietic stem cell niches in physiology and pathology.
Dissociable dopaminergic control of saccadic target selection and its implications for reward modulation
Authors: Soltani Alireza , Noudoost Behrad , Moore Tirin
Published: February 2013

To investigate mechanisms by which reward modulates target selection, we studied the behavioral effects of perturbing dopaminergic activity within the frontal eye field (FEF) of monkeys performing a saccadic choice task and simulated the effects using a plausible cortical network. We found that manipulation of FEF activity either by blocking D1 receptors (D1Rs) or by stimulating D2 receptors (D2Rs) increased the tendency to choose targets in the response field of the affected site. However, the D1R manipulation decreased the tendency to repeat choices on subsequent trials, whereas the D2R manipulation increased that tendency. Moreover, the amount of shift in target selection resulting from the two manipulations correlated in opposite ways with the baseline stochasticity of choice behavior. Our network simulation results suggest that D1Rs influence target selection mainly through their effects on the strength of inputs to the FEF and on recurrent connectivity, whereas D2Rs influence the excitability of FEF output neurons. Altogether, these results reveal dissociable dopaminergic mechanisms influencing target selection and suggest how reward can influence adaptive choice behavior via prefrontal dopamine.
Quantitative analysis of the time course of Aβ oligomerization and subsequent growth steps using tetramethylrhodamine-labeled Aβ
Authors: Garai Kanchan , Frieden Carl
Published: February 2013

Although amyloid β (Aβ) is a critical player in the pathology of Alzheimer’s disease, there is currently little Information on the rate and extent of formation of oligomers that lead to the presence of Aβ fibrils observed in amyloid plaques. Here we describe a unique method to monitor the full time course of Aβ aggregation. In this method, Aβ is labeled with tetramethylrhodamine at a lysine residue on the N-terminal end. During aggregation, the fluorescence is quenched in a time-dependent manner in three distinct phases: an early oligomerization phase, an intermediate phase, and a growth phase. The oligomerization phase can be characterized as a monomer-dimer-trimer process for which we have determined the rate and equilibrium constants. The rate constants differ markedly between Aβ
1–42
and Aβ
1–40
, with Aβ
1–42
showing a greater oligomerization propensity. The intermediate phase reflects slow clustering and reorganization of the oligomers, whereas the growth phase ultimately results in the formation of fibrillar material. The data are consistent with a conformational change being an important rate-limiting step in the overall aggregation process. The rates of all phases are highly sensitive to temperature and pH, with the pH-dependent data indicating important roles for lysine and histidine residues. From the temperature-dependent data, activation energies of oligomerization and fibrillization are estimated to be 5.5 and 12.1 kCal/mol, respectively. The methodologies presented here are simple and can be applied to other amyloidogenic peptides or proteins.
Long noncoding RNAs regulate adipogenesis
Authors: Sun Lei , Goff Loyal A. , Trapnell Cole , Alexander Ryan , Lo Kinyui Alice , Hacisuleyman Ezgi , Sauvageau Martin , Tazon-Vega Barbara , Kelley David R. , Hendrickson David G. , Yuan Bingbing , Kellis Manolis , Lodish Harvey F. , Rinn John L.
Published: February 2013

The prevalence of obesity has led to a surge of interest in understanding the detailed mechanisms underlying adipocyte development. Many protein-coding genes, mRNAs, and microRNAs have been implicated in adipocyte development, but the global expression patterns and functional contributions of long noncoding RNA (lncRNA) during adipogenesis have not been explored. Here we profiled the transcriptome of primary brown and white adipocytes, preadipocytes, and cultured adipocytes and identified 175 lncRNAs that are specifically regulated during adipogenesis. Many lncRNAs are adipose-enriched, strongly induced during adipogenesis, and bound at their promoters by key transcription factors such as peroxisome proliferator-activated receptor γ (PPARγ) and CCAAT/enhancer-binding protein α (CEBPα). RNAi-mediated loss of function screens identified functional lncRNAs with varying impact on adipogenesis. Collectively, we have identified numerous lncRNAs that are functionally required for proper adipogenesis.
Genomic responses in mouse models poorly mimic human inflammatory diseases
Authors: Seok Junhee , Warren H. Shaw , Cuenca Alex G. , Mindrinos Michael N. , Baker Henry V. , Xu Weihong , Richards Daniel R. , McDonald-Smith Grace P. , Gao Hong , Hennessy Laura , Finnerty Celeste C. , López Cecilia M. , Honari Shari , Moore Ernest E. , Minei Joseph P. , Cuschieri Joseph , Bankey Paul E. , Johnson Jeffrey L. , Sperry Jason , Nathens Avery B. , Billiar Timothy R. , West Michael A. , Jeschke Marc G. , Klein Matthew B. , Gamelli Richard L. , Gibran Nicole S. , Brownstein Bernard H. , Miller-Graziano Carol , Calvano Steve E. , Mason Philip H. , Cobb J. Perren , Rahme Laurence G. , Lowry Stephen F. , Maier Ronald V. , Moldawer Lyle L. , Herndon David N. , Davis Ronald W. , Xiao Wenzhong , Tompkins Ronald G. ,   the Inflammation and Host Response to Injury, Large Scale Collaborative Research Program, Abouhamze Amer , Balis Ulysses G. J. , Camp David G. , De Asit K. , Harbrecht Brian G. , Hayden Douglas L. , Kaushal Amit , O’Keefe Grant E. , Kotz Kenneth T. , Qian Weijun , Schoenfeld David A. , Shapiro Michael B. , Silver Geoffrey M. , Smith Richard D. , Storey John D. , Tibshirani Robert , Toner Mehmet , Wilhelmy Julie , Wispelwey Bram , Wong Wing H
Published: February 2013

A cornerstone of modern biomedical research is the use of mouse models to explore basic pathophysiological mechanisms, evaluate new therapeutic approaches, and make go or no-go decisions to carry new drug candidates forward into clinical trials. Systematic studies evaluating how well murine models mimic human inflammatory diseases are nonexistent. Here, we show that, although acute inflammatory stresses from different etiologies result in highly similar genomic responses in humans, the responses in corresponding mouse models correlate poorly with the human conditions and also, one another. Among genes changed significantly in humans, the murine orthologs are close to random in matching their human counterparts (e.g.,
R
2
between 0.0 and 0.1). In addition to improvements in the current animal model systems, our study supports higher priority for translational medical research to focus on the more complex human conditions rather than relying on mouse models to study human inflammatory diseases.
Astrocyte pathology and the absence of non-cell autonomy in an induced pluripotent stem cell model of TDP-43 proteinopathy
Authors: Serio Andrea , Bilican Bilada , Barmada Sami J. , Ando Dale Michael , Zhao Chen , Siller Rick , Burr Karen , Haghi Ghazal , Story David , Nishimura Agnes Lumi , Carrasco Monica A. , Phatnani Hemali P. , Shum Carole , Wilmut Ian , Maniatis Tom , Shaw Christopher E. , Finkbeiner Steven , Chandran Siddharthan
Published: February 2013

Glial proliferation and activation are associated with disease progression in amyotrophic lateral sclerosis (ALS) and frontotemporal lobar dementia. In this study, we describe a unique platform to address the question of cell autonomy in tran
s
active response DNA-binding protein (TDP-43) proteinopathies. We generated functional astroglia from human induced pluripotent stem cells carrying an ALS-causing TDP-43 mutation and show that mutant astrocytes exhibit increased levels of TDP-43, subcellular mislocalization of TDP-43, and decreased cell survival. We then performed coculture experiments to evaluate the effects of M337V astrocytes on the survival of wild-type and M337V TDP-43 motor neurons, showing that mutant TDP-43 astrocytes do not adversely affect survival of cocultured neurons. These observations reveal a significant and previously unrecognized glial cell-autonomous pathological phenotype associated with a pathogenic mutation in TDP-43 and show that TDP-43 proteinopathies do not display an astrocyte non-cell-autonomous component in cell culture, as previously described for SOD1 ALS. This study highlights the utility of induced pluripotent stem cell-based in vitro disease models to investigate mechanisms of disease in ALS and other TDP-43 proteinopathies.
Bipartite determinants mediate an evolutionarily conserved interaction between Cdc48 and the 20
S
peptidase
Authors: Barthelme Dominik , Sauer Robert T.
Published: February 2013

Proteasomes are essential and ubiquitous ATP-dependent proteases that function in eukarya, archaea, and some bacteria. These destructive but critically important proteolytic machines use a 20
S
core peptidase and a hexameric
A
TPase
a
ssociated with a variety of cellular
a
ctivities (AAA+) unfolding ring that unfolds and spools substrates into the peptidase chamber. In archaea, 20
S
can function with the AAA+ Cdc48 or proteasome-activating nucleotidase (PAN) unfoldases. Both interactions are stabilized by C-terminal tripeptides in AAA+ subunits that dock into pockets on the 20
S
periphery. Here, we provide evidence that archaeal Cdc48 also uses a distinct set of near-axial interactions to bind 20
S
and propose that similar dual determinants mediate PAN–20
S
interactions and Rpt
1
–6
–20
S
interactions in the 26
S
proteasome. Current dogma holds that the Rpt
1–6
unfolding ring of the 19
S
regulatory particle is the only AAA+ partner of eukaryotic 20
S
. By contrast, we show that mammalian Cdc48, a key player in cell-cycle regulation, membrane fusion, and endoplasmic-reticulum–associated degradation, activates mammalian 20
S
and find that a mouse Cdc48 variant supports protein degradation in combination with 20
S
. Our results suggest that eukaryotic Cdc48 orthologs function directly with 20
S
to maintain intracellular protein quality control.
Previously undescribed grass pollen antigens are the major inducers of T helper 2 cytokine-producing T cells in allergic individuals
Authors: Schulten Véronique , Greenbaum Jason A. , Hauser Michael , McKinney Denise M. , Sidney John , Kolla Ravi , Lindestam Arlehamn Cecilia S. , Oseroff Carla , Alam Rapheul , Broide David H. , Ferreira Fatima , Grey Howard M. , Sette Alessandro , Peters Bjoern
Published: February 2013

T cells play an important role in the pathogenesis of allergic diseases. However, the proteins considered as potential immunogens of allergenic T-cell responses have traditionally been limited to those that induce IgE responses. Timothy grass (TG) pollen is a well-studied inhaled allergen for which major IgE-reactive allergens have also been shown to trigger T helper 2 (Th2) responses. Here we examined whether other TG pollen proteins are recognized by Th2 responses independently of IgE reactivity. A TG pollen extract was analyzed by 2D gel electrophoresis and IgE/IgG immunoblots using pooled sera from allergic donors. Mass spectrometry of selected protein spots in combination with de novo sequencing of the whole TG pollen transcriptome identified 93 previously undescribed proteins for further study, 64 of which were not targeted by IgE. Predicted MHC binding peptides from the previoulsy undescribed TG proteins were screened for T-cell reactivity in peripheral blood mononuclear cells from allergic donors. Strong IL-5 production was detected in response to peptides from several of the previously undescribed proteins, most of which were not targeted by IgE. Responses against the dominant undescribed epitopes were associated with the memory T-cell subset and could even be detected directly ex vivo after Th2 cell enrichment. These findings demonstrate that a combined unbiased transcriptomic, proteomic, and immunomic approach identifies a greatly broadened repertoire of protein antigens targeted by T cells involved in allergy pathogenesis. The discovery of proteins that induce Th2 cells but are not IgE reactive may allow the development of safer immunotherapeutic strategies.
Diversification of rhacophorid frogs provides evidence for accelerated faunal exchange between India and Eurasia during the Oligocene
Authors: Li Jia-Tang , Li Yang , Klaus Sebastian , Rao Ding-Qi , Hillis David M. , Zhang Ya-Ping
Published: February 2013

The accretion of the Indian subcontinent to Eurasia triggered a massive faunal and floral exchange, with Gondwanan taxa entering into Asia and vice versa. The traditional view on the Indian–Asian collision assumes contact of the continental plates during the Early Eocene. Many biogeographic studies rely on this assumption. However, the exact mode and timing of this geological event is still under debate. Here we address, based on an extensive phylogenetic analysis of rhacophorid tree frogs, if there was already a Paleogene biogeographic link between Southeast Asia and India; in which direction faunal exchange occurred between India and Eurasia within the Rhacophoridae; and if the timing of the faunal exchange correlates with one of the recently suggested geological models. Rhacophorid tree frogs showed an early dispersal from India to Asia between 46 and 57 Ma, as reconstructed from the fossil record. During the Middle Eocene, however, faunal exchange ceased, followed by increase of rhacophorid dispersal events between Asia and the Indian subcontinent during the Oligocene that continued until the Middle Miocene. This corroborates recent geological models that argue for a much later final collision between the continental plates. We predict that the Oligocene faunal exchange between the Indian subcontinent and Asia, as shown here for rhacophorid frogs, also applies for other nonvolant organisms with an Indian–Asian distribution, and suggest that previous studies that deal with this faunal interchange should be carefully reinvestigated.
Distress Tolerance and Perceived Barriers to Smoking Cessation
Authors: Kraemer Kristen M. , McLeish Alison C. , Jeffries Emily R. , Avallone Kimberly M. , Luberto Christina M.
Published: February 2013

Background

The present study examined the role of emotional distress tolerance (DT) in predicting barriers to smoking cessation and number of quit attempts.

Methods

The sample consisted of regular daily smokers ( N = 126; 37 females; M age = 36.51, SD = 13.05) who completed self-report measures on affect and smoking.

Results

After controlling for daily smoking rate and anxiety sensitivity, emotional DT significantly predicted internal barriers to cessation (6.9% unique variance) but not external or addiction-related barriers to cessation. Inconsistent with prediction, emotional DT did not significantly predict number of quit attempts.

Conclusions

These results suggest that individuals who are low in emotional DT believe that quitting smoking will be difficult because it takes away an important affect regulation strategy, and there may be utility in targeting emotional DT in smoking cessation interventions.
A Descriptive Study of Adverse Events from Clenbuterol Misuse and Abuse for Weight Loss and Bodybuilding
Authors: Spiller Henry A. , James Kyla J. , Scholzen Steven , Borys Douglas J.
Published: February 2013

Background

Clenbuterol is a β2-agonist approved in the United States for veterinary use in nonfood animals. Clenbuterol use is emerging among bodybuilders and fitness enthusiasts attracted to the hypertrophic and lipolytic effects.

Cases

This was a retrospective chart review of clenbuterol exposures reported to 2 poison control centers. Misuse of clenbuterol for weight loss and bodybuilding was reported in 11 of 13 clenbuterol users. Reported clinical effects included tachycardia, widened pulse pressure, tachypnea, hypokalemia, hyperglycemia, ST changes on electrocardiogram (ECG), elevated troponin, elevated creatine phosphokinase (CPK), palpitations, chest pain, and tremor. Measured serum clenbuterol concentration was 2983 pg/mL post 4.5 mg ingestion. Coingestants included T3 and anabolic steroids. Treatments included activated charcoal, benzodiazepines, β-blockers, potassium replacement, and intravenous (IV) fluid.

Conclusions

There is an increasing use of the Internet for illicit drug use for bodybuilding and weight loss purposes. These patients may not present as the stereotype of illicit drug abusers, but as healthy athletic low-risk patients. Clinical effects persisted greater than 24 hours with evidence of myocardial injury in 2 patients. Clenbuterol is increasingly being abused within the bodybuilding subculture. These cases illustrate the hidden dangers of clenbuterol abuse among bodybuilders and fitness enthusiasts.
Clathrin and AP2 are required for PtdIns(4,5)P2-mediated formation of LRP6 signalosomes
Authors: Kim Ingyu , Pan Weijun , Jones Sara A. , Zhang Youxin , Zhuang Xiaowei , Wu Dianqing
Published: February 2013

Canonical Wnt signaling is initiated by the binding of Wnt proteins to their receptors, low-density lipoprotein-related protein 5 and 6 (LRP5/6) and frizzled proteins, leading to phosphatidylinositol (4,5)bisphosphate (PtdIns(4,5)P2) production, signalosome formation, and LRP phosphorylation. However, the mechanism by which PtdIns(4,5)P2 regulates the signalosome formation remains unclear. Here we show that clathrin and adaptor protein 2 (AP2) were part of the LRP6 signalosomes. The presence of clathrin and AP2 in the LRP6 signalosomes depended on PtdIns(4,5)P2, and both clathrin and AP2 were required for the formation of LRP6 signalosomes. In addition, WNT3A-induced LRP6 signalosomes were primarily localized at cell surfaces, and WNT3A did not induce marked LRP6 internalization. However, rapid PtdIns(4,5)P2 hydrolysis induced artificially after WNT3A stimulation could lead to marked LRP6 internalization. Moreover, we observed WNT3A-induced LRP6 and clathrin clustering at cell surfaces using super-resolution fluorescence microscopy. Therefore, we conclude that PtdIns(4,5)P2 promotes the assembly of LRP6 signalosomes via the recruitment of AP2 and clathrin and that LRP6 internalization may not be a prerequisite for Wnt signaling to β-catenin stabilization.
SecYEG activates GTPases to drive the completion of cotranslational protein targeting
Authors: Akopian David , Dalal Kush , Shen Kuang , Duong Franck , Shan Shu-ou
Published: February 2013

Signal recognition particle (SRP) and its receptor (SR) comprise a highly conserved cellular machine that cotranslationally targets proteins to a protein-conducting channel, the bacterial SecYEG or eukaryotic Sec61p complex, at the target membrane. Whether SecYEG is a passive recipient of the translating ribosome or actively regulates this targeting machinery remains unclear. Here we show that SecYEG drives conformational changes in the cargo-loaded SRP–SR targeting complex that activate it for GTP hydrolysis and for handover of the translating ribosome. These results provide the first evidence that SecYEG actively drives the efficient delivery and unloading of translating ribosomes at the target membrane.
Innate Stat3-mediated induction of the antimicrobial protein Reg3γ is required for host defense against MRSA pneumonia
Authors: Choi Sun-Mi , McAleer Jeremy P. , Zheng Mingquan , Pociask Derek A. , Kaplan Mark H. , Qin Shulin , Reinhart Todd A. , Kolls Jay K.
Published: February 2013

Pulmonary Staphylococcus aureus (SA) infections are a public health concern and a major complication of hyper-IgE syndrome, caused by mutations in STAT3. In contrast to previous findings of skin infection, we observed that clearance of SA from the lung did not require T, B, or NK cells but did require Stat3 activation. Immunohistochemistry showed robust Stat3 phosphorylation in the lung epithelium. We identified that a critical Stat3 target gene in lung epithelium is Reg3g (regenerating islet-derived 3 γ), a gene which is highly expressed in gastrointestinal epithelium but whose role in pulmonary host defense is uncharacterized. Stat3 regulated Reg3g transcription through direct binding at the Reg3g promoter region. Recombinant Reg3γ bound to SA and had both bacteriostatic and bactericidal activity in a dose-dependent fashion. Stat3 inhibition in vivo reduced Reg3g transcripts in the lung, and more importantly, recombinant Reg3γ rescued mice from defective SA clearance. These findings reveal an antibacterial function for lung epithelium through Stat3-mediated induction of Reg3γ.