bluuebunny/crossref_metadata_2025 huggingface dataset:
Structural insights into the interaction and disease mechanism of neurodegenerative disease-associated optineurin and TBK1 proteins
Authors: Li Faxiang , Xie Xingqiao , Wang Yingli , Liu Jianping , Cheng Xiaofang , Guo Yujiao , Gong Yukang , Hu Shichen , Pan Lifeng
Published: September 2016

Optineurin is an important autophagy receptor involved in several selective autophagy processes, during which its function is regulated by TBK1. Mutations of optineurin and TBK1 are both associated with neurodegenerative diseases. However, the mechanistic basis underlying the specific interaction between optineurin and TBK1 is still elusive. Here we determine the crystal structures of optineurin/TBK1 complex and the related NAP1/TBK1 complex, uncovering the detailed molecular mechanism governing the optineurin and TBK1 interaction, and revealing a general binding mode between TBK1 and its associated adaptor proteins. In addition, we demonstrate that the glaucoma-associated optineurin E50K mutation not only enhances the interaction between optineurin and TBK1 but also alters the oligomeric state of optineurin, and the ALS-related TBK1 E696K mutation specifically disrupts the optineurin/TBK1 complex formation but has little effect on the NAP1/TBK1 complex. Thus, our study provides mechanistic insights into those currently known disease-causing optineurin and TBK1 mutations found in patients.
Thermal control of sequential on-surface transformation of a hydrocarbon molecule on a copper surface
Authors: Kawai Shigeki , Haapasilta Ville , Lindner Benjamin D. , Tahara Kazukuni , Spijker Peter , Buitendijk Jeroen A. , Pawlak Rémy , Meier Tobias , Tobe Yoshito , Foster Adam S. , Meyer Ernst
Published: September 2016

On-surface chemical reactions hold the potential for manufacturing nanoscale structures directly onto surfaces by linking carbon atoms in a single-step reaction. To fabricate more complex and functionalized structures, the control of the on-surface chemical reactions must be developed significantly. Here, we present a thermally controlled sequential three-step chemical transformation of a hydrocarbon molecule on a Cu(111) surface. With a combination of high-resolution atomic force microscopy and first-principles computations, we investigate the transformation process in step-by-step detail from the initial structure to the final product via two intermediate states. The results demonstrate that surfaces can be used as catalysing templates to obtain compounds, which cannot easily be synthesized by solution chemistry.
A broadly neutralizing anti-influenza antibody reveals ongoing capacity of haemagglutinin-specific memory B cells to evolve
Authors: Fu Ying , Zhang Zhen , Sheehan Jared , Avnir Yuval , Ridenour Callie , Sachnik Thomas , Sun Jiusong , Hossain M. Jaber , Chen Li-Mei , Zhu Quan , Donis Ruben O. , Marasco Wayne A.
Published: September 2016

Understanding the natural evolution and structural changes involved in broadly neutralizing antibody (bnAb) development holds great promise for improving the design of prophylactic influenza vaccines. Here we report an haemagglutinin (HA) stem-directed bnAb, 3I14, isolated from human memory B cells, that utilizes a heavy chain encoded by the IGHV3-30 germline gene. MAb 3I14 binds and neutralizes groups 1 and 2 influenza A viruses and protects mice from lethal challenge. Analysis of VH and VL germline back-mutants reveals binding to H3 and H1 but not H5, which supports the critical role of somatic hypermutation in broadening the bnAb response. Moreover, a single VLD94N mutation improves the affinity of 3I14 to H5 by nearly 10-fold. These data provide evidence that memory B cell evolution can expand the HA subtype specificity. Our results further suggest that establishing an optimized memory B cell pool should be an aim of ‘universal’ influenza vaccine strategies.
Central relay of bitter taste to the protocerebrum by peptidergic interneurons in the Drosophila brain
Authors: Hückesfeld Sebastian , Peters Marc , Pankratz Michael J.
Published: September 2016

Bitter is a taste modality associated with toxic substances evoking aversive behaviour in most animals, and the valence of different taste modalities is conserved between mammals and Drosophila. Despite knowledge gathered in the past on the peripheral perception of taste, little is known about the identity of taste interneurons in the brain. Here we show that hugin neuropeptide-containing neurons in the Drosophila larval brain are necessary for avoidance behaviour to caffeine, and when activated, result in cessation of feeding and mediates a bitter taste signal within the brain. Hugin neuropeptide-containing neurons project to the neurosecretory region of the protocerebrum and functional imaging demonstrates that these neurons are activated by bitter stimuli and by activation of bitter sensory receptor neurons. We propose that hugin neurons projecting to the protocerebrum act as gustatory interneurons relaying bitter taste information to higher brain centres in Drosophila larvae.
Increased water salinity applied to tomato plants accelerates the development of the leaf miner Tuta absoluta through bottom-up effects
Authors: Han Peng , Wang Zhi-jian , Lavoir Anne-Violette , Michel Thomas , Seassau Aurélie , Zheng Wen-yan , Niu Chang-ying , Desneux Nicolas
Published: September 2016

Variation in resource inputs to plants may trigger bottom-up effects on herbivorous insects. We examined the effects of water input: optimal watervs. limited water; water salinity: withvs.without addition of 100 mM NaCl; and their interactions on tomato plants (Solanum lycopersicum), and consequently, the bottom-up effects on the tomato leaf miner,Tuta absoluta(Meytick) (Lepidoptera: Gelechiidae). Plant growth was significantly impeded by limited water input and NaCl addition. In terms of leaf chemical defense, the production of tomatidine significantly increased with limited water and NaCl addition, and a similar but non-significant trend was observed for the other glycoalkaloids.Tuta absolutasurvival did not vary with the water and salinity treatments, but the treatment “optimal water-high salinity” increased the development rate without lowering pupal mass. Our results suggest that caution should be used in the IPM program againstT. absolutawhen irrigating tomato crops with saline water.
A HTML5 open source tool to conduct studies based on Libet’s clock paradigm
Authors: Garaizar Pablo , Cubillas Carmelo P. , Matute Helena
Published: September 2016

Libet’s clock is a well-known procedure in experiments in psychology and neuroscience. Examples of its use include experiments exploring the subjective sense of agency, action-effect binding, and subjective timing of conscious decisions and perceptions. However, the technical details of the apparatus used to conduct these types of experiments are complex, and are rarely explained in sufficient detail as to guarantee an exact replication of the procedure. With this in mind, we developed Labclock Web, a web tool designed to conduct online and offline experiments using Libet’s clock. After describing its technical features, we explain how to configure specific experiments using this tool. Its degree of accuracy and precision in the presentation of stimuli has been technically validated, including the use of two cognitive experiments conducted with voluntary participants who performed the experiment both in our laboratory and via the Internet. Labclock Web is distributed without charge under a free software license (GPLv3) since one of our main objectives is to facilitate the replication of experiments and hence the advancement of knowledge in this area.
Binding affinity of amyloid oligomers to cellular membranes is a generic indicator of cellular dysfunction in protein misfolding diseases
Authors: Evangelisti Elisa , Cascella Roberta , Becatti Matteo , Marrazza Giovanna , Dobson Christopher M. , Chiti Fabrizio , Stefani Massimo , Cecchi Cristina
Published: September 2016

The conversion of peptides or proteins from their soluble native states into intractable amyloid deposits is associated with a wide range of human disorders. Misfolded protein oligomers formed during the process of aggregation have been identified as the primary pathogenic agents in many such conditions. Here, we show the existence of a quantitative relationship between the degree of binding to neuronal cells of different types of oligomers formed from a model protein, HypF-N, and the GM1 content of the plasma membranes. In addition, remarkably similar behavior is observed for oligomers of the Aβ42 peptide associated with Alzheimer’s disease. Further analysis has revealed the existence of a linear correlation between the level of the influx of Ca2+ across neuronal membranes that triggers cellular damage, and the fraction of oligomeric species bound to the membrane. Our findings indicate that the susceptibility of neuronal cells to different types of misfolded oligomeric assemblies is directly related to the extent of binding of such oligomers to the cellular membrane.
Microwave ablation of hepatocellular carcinoma as first-line treatment: long term outcomes and prognostic factors in 221 patients
Authors: Wang Tao , Lu Xiao-Jie , Chi Jia-Chang , Ding Min , Zhang Yuan , Tang Xiao-Yin , Li Ping , Zhang Li , Zhang Xiao-Yu , Zhai Bo
Published: September 2016

This retrospective study aimed at evaluating the long-term outcomes and prognostic factors of microwave ablation (MWA) as a first-line treatment for hepatocellular carcinoma (HCC). 221 consecutive patients receiving MWA in our center between October 11, 2010 and December 31, 2013 were enrolled. Technique effectiveness was evaluated one month post-ablation. Initial complete ablation (CA1st) was gained in 201 (90.95%) patients, secondary CA (CA2nd) in 8 (3.62%) patients and the remaining 12 (5.43%) patients suffered from incomplete ablation (IA2nd) after two sessions of MWA. Patients with tumor size >5 cm were less likely to gain CA1st. Procedure-related complications were recorded and no procedure-related death occurred. 22 (10.4%) complications occurred with 8 (3.8%) being major ones. Tumor characteristics (size, number, location) do not significantly influence complication rates. After a median follow-up of 41.0 (ranging 25.0–63.5) months, the median RFS and OS was 14.0 months (95% CI: 9.254–18.746) and 41.0 months (95% CI: 33.741–48.259) respectively. Multivariate analysis identified two significant prognosticators (levels of alpha fetal protein [AFP] and gamma-glutamyl transpeptidase [GGT]) of RFS and five significant prognosticators (tumor number, tumor size, AFP, GGT and recurrence type) of OS. In conclusion, MWA provides high technique effectiveness rate and is well tolerated in patients with HCC as a first-line treatment.
The multifaceted RisA regulon of Bordetella pertussis
Authors: Coutte Loïc , Huot Ludovic , Antoine Rudy , Slupek Stephanie , Merkel Tod J. , Chen Qing , Stibitz Scott , Hot David , Locht Camille
Published: September 2016

The whooping cough agentBordetella pertussisregulates the production of its virulence factors by the BvgA/S system. Phosphorylated BvgA activates the virulence-activated genes (vags) and represses the expression of the virulence-repressed genes (vrgs) via the activation of thebvgRgene. In modulating conditions, with MgSO4, the BvgA/S system is inactive, and thevrgs are expressed. Here, we show that the expression of almost allvrgs depends on RisA, another transcriptional regulator. We also show that somevags are surprisingly no longer modulated by MgSO4in therisA−background. RisA also regulates the expression of other genes, including chemotaxis and flagellar operons, iron-regulated genes, and genes of unknown function, which may or may not be controlled by BvgA/S. We identified RisK as the likely cognate RisA kinase and found that it is important for expression of most, but not all RisA-regulated genes. This was confirmed using the phosphoablative RisAD60N and the phosphomimetic RisAD60E analogues. Thus the RisA regulon adds a new layer of complexity toB. pertussisvirulence gene regulation.
Molecular organization, localization and orientation of antifungal antibiotic amphotericin B in a single lipid bilayer
Authors: Grudzinski Wojciech , Sagan Joanna , Welc Renata , Luchowski Rafal , Gruszecki Wieslaw I.
Published: September 2016

Amphotericin B is a popular antifungal antibiotic, a gold standard in treatment of systemic mycotic infections, due to its high effectiveness. On the other hand, applicability of the drug is limited by its considerable toxicity to patients. Biomembranes are a primary target of physiological activity of amphotericin B and both the pharmacologically desired and toxic side effects of the drug relay on its molecular organization in the lipid phase. In the present work, molecular organization, localization and orientation of amphotericin B, in a single lipid bilayer system, was analysed simultaneously, thanks to application of a confocal fluorescence lifetime imaging microscopy of giant unilamellar vesicles. The results show that the presence of sterols, in the lipid phase, promotes formation of supramolecular structures of amphotericin B and their penetration into the membrane hydrophobic core. The fact that such an effect is substantially less pronounced in the case ofcholesterol than ergosterol, the sterol of fungal membranes, provides molecular insight into the selectivity of the drug.
The yeast Aft2 transcription factor determines selenite toxicity by controlling the low affinity phosphate transport system
Authors: Pérez-Sampietro María , Serra-Cardona Albert , Canadell David , Casas Celia , Ariño Joaquín , Herrero Enrique
Published: September 2016

The yeast Saccharomyces cerevisiae is employed as a model to study the cellular mechanisms of toxicity and defense against selenite, the most frequent environmental selenium form. We show that yeast cells lacking Aft2, a transcription factor that together with Aft1 regulates iron homeostasis, are highly sensitive to selenite but, in contrast to aft1 mutants, this is not rescued by iron supplementation. The absence of Aft2 strongly potentiates the transcriptional responses to selenite, particularly for DNA damage- and oxidative stress-responsive genes, and results in intracellular hyperaccumulation of selenium. Overexpression of PHO4, the transcriptional activator of the PHO regulon under low phosphate conditions, partially reverses sensitivity and hyperaccumulation of selenite in a way that requires the presence of Spl2, a Pho4-controlled protein responsible for post-transcriptional downregulation of the low-affinity phosphate transporters Pho87 and Pho90. SPL2 expression is strongly downregulated in aft2 cells, especially upon selenite treatment. Selenite hypersensitivity of aft2 cells is fully rescued by deletion of PHO90, suggesting a major role for Pho90 in selenite uptake. We propose that the absence of Aft2 leads to enhanced Pho90 function, involving both Spl2-dependent and independent events and resulting in selenite hyperaccumulation and toxicity.
Cold tolerance is unaffected by oxygen availability despite changes in anaerobic metabolism
Authors: Boardman Leigh , Sørensen Jesper G. , Koštál Vladimír , Šimek Petr , Terblanche John S.
Published: September 2016

Insect cold tolerance depends on their ability to withstand or repair perturbations in cellular homeostasis caused by low temperature stress. Decreased oxygen availability (hypoxia) can interact with low temperature tolerance, often improving insect survival. One mechanism proposed for such responses is that whole-animal cold tolerance is set by a transition to anaerobic metabolism. Here, we provide a test of this hypothesis in an insect model system (Thaumatotibia leucotreta) by experimental manipulation of oxygen availability while measuring metabolic rate, critical thermal minimum (CTmin), supercooling point and changes in 43 metabolites in moth larvae at three key timepoints (before, during and after chill coma). Furthermore, we determined the critical oxygen partial pressure below which metabolic rate was suppressed (c. 4.5 kPa). Results showed that altering oxygen availability did not affect (non-lethal) CTminnor (lethal) supercooling point. Metabolomic profiling revealed the upregulation of anaerobic metabolites and alterations in concentrations of citric acid cycle intermediates during and after chill coma exposure. Hypoxia exacerbated the anaerobic metabolite responses induced by low temperatures. These results suggest that cold tolerance ofT. leucotretalarvae is not set by oxygen limitation, and that anaerobic metabolism in these larvae may contribute to their ability to survive in necrotic fruit.
Aspect-ratio driven evolution of high-order resonant modes and near-field distributions
in localized surface phonon polariton nanostructures
Authors: Ellis Chase T. , Tischler Joseph G. , Glembocki Orest J. , Bezares Francisco J. , Giles Alexander J. , Kasica Richard , Shirey Loretta , Owrutsky Jeffrey C. , Chigrin Dmitry N. , Caldwell Joshua D.
Published: September 2016

Polar dielectrics have garnered much attention as an alternative to plasmonic metals
in the mid- to long-wave infrared spectral regime due to their low optical losses.
As such, nanoscale resonators composed of these materials demonstrate figures of
merit beyond those achievable in plasmonic equivalents. However, until now, only
low-order, phonon-mediated, localized polariton resonances, known as surface phonon
polaritons (SPhPs), have been observed in polar dielectric optical resonators. In
the present work, we investigate the excitation of 16 distinct high-order,
multipolar, localized surface phonon polariton resonances that are optically excited
in rectangular pillars etched into a semi-insulating silicon carbide substrate. By
elongating a single pillar axis we are able to significantly modify the far- and
near-field properties of localized SPhP resonances, opening the door to realizing
narrow-band infrared sources with tailored radiation patterns. Such control of the
near-field behavior of resonances can also impact surface enhanced infrared optical
sensing, which is mediated by polarization selection rules, as well as the
morphology and strength of resonator hot spots. Furthermore, through the careful
choice of polar dielectric material, these results can also serve as the guiding
principles for the generalized design of optical devices that operate from the mid-
to far-infrared.
PI3 Kinase Pathway and MET Inhibition is Efficacious in Malignant Pleural Mesothelioma
Authors: Kanteti Rajani , Riehm Jacob J. , Dhanasingh Immanuel , Lennon Frances E. , Mirzapoiazova Tamara , Mambetsariev Bolot , Kindler Hedy L. , Salgia Ravi
Published: September 2016

Malignant pleural mesothelioma (MPM) is an aggressive cancer that is commonly associated with prior asbestos exposure. Receptor tyrosine kinases (RTKs) such as MET and its downstream target PI3K are overexpressed and activated in a majority of MPMs. Here, we studied the combinatorial therapeutic efficacy of the MET/ALK inhibitor crizotinib, with either a pan-class I PI3K inhibitor, BKM120, or with a PI3K/mTOR dual inhibitor, GDC-0980, in mesothelioma. Cell viability results showed that MPM cells were highly sensitive to crizotinib, BKM120 and GDC-0980 when used individually and their combination was more effective in suppressing growth. Treatment of MPM cells with these inhibitors also significantly decreased cell migration, and the combination of them was synergistic. Treatment with BKM120 alone or in combination with crizotinib induced G2-M arrest and apoptosis. Both crizotinib and BKM120 strongly inhibited the activity of MET and PI3K as evidenced by the decreased phosphorylation of MET, AKT and ribosomal S6 kinase. Using a PDX mouse model, we showed that a combination of crizotinib with BKM120 was highly synergetic in inhibiting MPM tumor growth. In conclusion our findings suggest that dual inhibition of PI3K and MET pathway is an effective strategy in treating MPM as compared to a single agent.
Trp53 deficient mice predisposed to preterm birth display region-specific lipid alterations at the embryo implantation site
Authors: Lanekoff Ingela , Cha Jeeyeon , Kyle Jennifer E. , Dey Sudhansu K. , Laskin Julia , Burnum-Johnson Kristin E.
Published: September 2016

Here we demonstrate that conditional deletion of mouse uterine Trp53 (p53d/d), molecularly linked to mTORC1 activation and causally linked to premature uterine senescence and preterm birth, results in aberrant lipid signatures within the heterogeneous cell types of embryo implantation sites on day 8 of pregnancy. In situ nanospray desorption electrospray ionization mass spectrometry imaging (nano-DESI MSI) was used to characterize the molecular speciation of free fatty acids, monoacylglycerol species, unmodified and oxidized phosphatidylcholine (PC/Ox-PC), and diacylglycerol (DG) species within implantation sites of p53d/d mice and floxed littermates. Implantation sites from p53d/d mice exhibited distinct spatially resolved changes demonstrating accumulation of DG species, depletion of Ox-PC species, and increase in species with more unsaturated acyl chains, including arachidonic and docosahexaenoic acid. Understanding abnormal changes in the abundance and localization of individual lipid species early in the progression to premature birth is an important step toward discovering novel targets for treatments and diagnosis.
HSCCC-based strategy for preparative separation of in vivo metabolites after administration of an herbal medicine: Saussurea laniceps, a case study
Authors: Yi Tao , Zhu Lin , Zhu Guo-Yuan , Tang Yi-Na , Xu Jun , Fan Jia-Yi , Zhao Zhong-Zhen , Chen Hu-Biao
Published: September 2016

This paper reports a novel strategy based on high-speed counter-current chromatography (HSCCC) technique to separate in vivo metabolites from refined extract of urine after administration of an herbal medicine. Saussurea laniceps (SL) was chosen as a model herbal medicine to be used to test the feasibility of our proposed strategy. This strategy succeeded in the case of separating four in vivo metabolites of SL from the urine of rats. Briefly, after oral administration of SL extract to three rats for ten days (2.0 g/kg/d), 269.1 mg of umbelliferone glucuronide (M1, purity, 92.5%), 432.5 mg of scopoletin glucuronide (M2, purity, 93.2%), 221.4 mg of scopoletin glucuronide (M3, purity, 92.9%) and 319.0 mg of scopoletin glucuronide (M4, purity, 90.4%) were separated from 420 mL of the rat urine by HSCCC using a two-phase solvent system composed of methyl tert-butyl ether–n-butanol–acetonitrile–water (MTBE–n-BuOH–ACN–H2O) at a volume ratio of 10:30:11:49. The chemical structures of the four metabolites, M1 to M4, were confirmed by MS and 1H, 13C NMR. As far as we know, this is the first report of the successful separation of in vivo metabolites by HSCCC after administration of an herbal medicine.
Precise Characterisation of Molecular Orientation in a Single Crystal Field-Effect Transistor Using Polarised Raman Spectroscopy
Authors: Wood Sebastian , Rigas Grigorios-Panagiotis , Zoladek-Lemanczyk Alina , Blakesley James C. , Georgakopoulos Stamatis , Mas-Torrent Marta , Shkunov Maxim , Castro Fernando A.
Published: September 2016

Charge transport in organic semiconductors is strongly dependent on the molecular orientation and packing, such that manipulation of this molecular packing is a proven technique for enhancing the charge mobility in organic transistors. However, quantitative measurements of molecular orientation in micrometre-scale structures are experimentally challenging. Several research groups have suggested polarised Raman spectroscopy as a suitable technique for these measurements and have been able to partially characterise molecular orientations using one or two orientation parameters. Here we demonstrate a new approach that allows quantitative measurements of molecular orientations in terms of three parameters, offering the complete characterisation of a three-dimensional orientation. We apply this new method to organic semiconductor molecules in a single crystal field-effect transistor in order to correlate the measured orientation with charge carrier mobility measurements. This approach offers the opportunity for micrometre resolution (diffraction limited) spatial mapping of molecular orientation using bench-top apparatus, enabling a rational approach towards controlling this orientation to achieve optimum device performance.
Does cryptic microbiota mitigate pine resistance to an invasive beetle-fungus complex? Implications for invasion potential
Authors: Cheng Chihang , Xu Letian , Xu Dandan , Lou Qiaozhe , Lu Min , Sun Jianghua
Published: September 2016

Microbial symbionts are known to assist exotic pests in their colonization of new host plants. However, there has been little evidence linking symbiotic invasion success to mechanisms for mitigation of native plant resistance. The red turpentine beetle (RTB) was introduced with a fungus, Leptographium procerum, to China from the United States and became a destructively invasive symbiotic complex in natural Pinus tabuliformis forests. Here, we report that three Chinese-resident fungi, newly acquired by RTB in China, induce high levels of a phenolic defensive chemical, naringenin, in pines. This invasive beetle-fungus complex is suppressed by elevated levels of naringenin. However, cryptic microbiotas in RTB galleries strongly degrade naringenin, and pinitol, the main soluble carbohydrate of P. tabuliformis, is retained in L. procerum-infected phloem and facilitate naringenin biodegradation by the microbiotas. These results demonstrate that cryptic microbiota mitigates native host plant phenolic resistance to an invasive symbiotic complex, suggesting a putative mechanism for reduced biotic resistance to symbiotic invasion.
Incorporation of Eu(III) into Calcite under Recrystallization conditions
Authors: Hellebrandt S. E. , Hofmann S. , Jordan N. , Barkleit A. , Schmidt M.
Published: September 2016

The interaction of calcite with trivalent europium under recrystallization conditions was studied on the molecular level using site-selective time-resolved laser fluorescence spectroscopy (TRLFS). We conducted batch studies with a reaction time from seven days up to three years with three calcite powders, which differed in their specific surface area, recrystallization rates and impurities content. With increase of the recrystallization rate incorporation of Eu3+ occurs faster and its speciation comes to be dominated by one species with its excitation maximum at 578.8 nm, so far not identified during previous investigations of this process under growth and phase transformation conditions. A long lifetime of 3750 μs demonstrates complete loss of hydration, consequently Eu must have been incorporated into the bulk crystal. The results show a strong dependence of the incorporation kinetics on the recrystallization rate of the different calcites. Furthermore the investigation of the effect of different background electrolytes (NaCl and KCl) demonstrate that the incorporation process under recrystallization conditions strongly depends on the availability of Na+. These findings emphasize the different retention potential of calcite as a primary and secondary mineral e.g. in a nuclear waste disposal site.
Failure mechanism of monolayer graphene under hypervelocity impact of spherical projectile
Authors: Xia Kang , Zhan Haifei , Hu De’an , Gu Yuantong
Published: September 2016

The excellent mechanical properties of graphene have enabled it as appealing candidate in the field of impact protection or protective shield. By considering a monolayer graphene membrane, in this work, we assessed its deformation mechanisms under hypervelocity impact (from 2 to 6 km/s), based on a serial of in silico studies. It is found that the cracks are formed preferentially in the zigzag directions which are consistent with that observed from tensile deformation. Specifically, the boundary condition is found to exert an obvious influence on the stress distribution and transmission during the impact process, which eventually influences the penetration energy and crack growth. For similar sample size, the circular shape graphene possesses the best impact resistance, followed by hexagonal graphene membrane. Moreover, it is found the failure shape of graphene membrane has a strong relationship with the initial kinetic energy of the projectile. The higher kinetic energy, the more number the cracks. This study provides a fundamental understanding of the deformation mechanisms of monolayer graphene under impact, which is crucial in order to facilitate their emerging future applications for impact protection, such as protective shield from orbital debris for spacecraft.
Cell wall degradation is required for normal starch mobilisation in barley endosperm
Authors: Andriotis Vasilios M. E. , Rejzek Martin , Barclay Elaine , Rugen Michael D. , Field Robert A. , Smith Alison M.
Published: September 2016

Starch degradation in barley endosperm provides carbon for early seedling growth, but the control of this process is poorly understood. We investigated whether endosperm cell wall degradation is an important determinant of the rate of starch degradation. We identified iminosugar inhibitors of enzymes that degrade the cell wall component arabinoxylan. The iminosugar 1,4-dideoxy-1, 4-imino-l-arabinitol (LAB) inhibits arabinoxylan arabinofuranohydrolase (AXAH) but does not inhibit the main starch-degrading enzymes α- and β-amylase and limit dextrinase. AXAH activity in the endosperm appears soon after the onset of germination and resides in dimers putatively containing two isoforms, AXAH1 and AXAH2. Upon grain imbibition, mobilisation of arabinoxylan and starch spreads across the endosperm from the aleurone towards the crease. The front of arabinoxylan degradation precedes that of starch degradation. Incubation of grains with LAB decreases the rate of loss of both arabinoxylan and starch, and retards the spread of both degradation processes across the endosperm. We propose that starch degradation in the endosperm is dependent on cell wall degradation, which permeabilises the walls and thus permits rapid diffusion of amylolytic enzymes. AXAH may be of particular importance in this respect. These results provide new insights into the mobilization of endosperm reserves to support early seedling growth.
Altered brain ion gradients following compensation for elevated CO2 are linked to behavioural alterations in a coral reef fish
Authors: Heuer R. M. , Welch M. J. , Rummer J. L. , Munday P. L. , Grosell M.
Published: September 2016

Neurosensory and behavioural disruptions are some of the most consistently reported responses upon exposure to ocean acidification-relevant CO2 levels, especially in coral reef fishes. The underlying cause of these disruptions is thought to be altered current across the GABAA receptor in neuronal cells due to changes in ion gradients (HCO3− and/or Cl−) that occur in the body following compensation for elevated ambient CO2. Despite these widely-documented behavioural disruptions, the present study is the first to pair a behavioural assay with measurements of relevant intracellular and extracellular acid-base parameters in a coral reef fish exposed to elevated CO2. Spiny damselfish (Acanthochromis polyacanthus) exposed to 1900 μatm CO2 for 4 days exhibited significantly increased intracellular and extracellular HCO3− concentrations and elevated brain pHi compared to control fish, providing evidence of CO2 compensation. As expected, high CO2 exposed damselfish spent significantly more time in a chemical alarm cue (CAC) than control fish, supporting a potential link between behavioural disruption and CO2 compensation. Using HCO3− measurements from the damselfish, the reversal potential for GABAA (EGABA) was calculated, illustrating that biophysical properties of the brain during CO2 compensation could change GABAA receptor function and account for the behavioural disturbances noted during exposure to elevated CO2.
Fluorescence imaging of chromosomal DNA using click chemistry
Authors: Ishizuka Takumi , Liu Hong Shan , Ito Kenichiro , Xu Yan
Published: September 2016

Chromosome visualization is essential for chromosome analysis and genetic diagnostics. Here, we developed a click chemistry approach for multicolor imaging of chromosomal DNA instead of the traditional dye method. We first demonstrated that the commercially available reagents allow for the multicolor staining of chromosomes. We then prepared two pro-fluorophore moieties that served as light-up reporters to stain chromosomal DNA based on click reaction and visualized the clear chromosomes in multicolor. We applied this strategy in fluorescence in situ hybridization (FISH) and identified, with high sensitivity and specificity, telomere DNA at the end of the chromosome. We further extended this approach to observe several basic stages of cell division. We found that the click reaction enables direct visualization of the chromosome behavior in cell division. These results suggest that the technique can be broadly used for imaging chromosomes and may serve as a new approach for chromosome analysis and genetic diagnostics.
Reproducible Ultrahigh SERS Enhancement in Single Deterministic Hotspots Using Nanosphere-Plane Antennas Under Radially Polarized Excitation
Authors: Long Jing , Yi Hui , Li Hongquan , Lei Zeyu , Yang Tian
Published: September 2016

Surface enhanced Raman scattering (SERS) in a nanometer size hotspot has empowered the investigation of chemical structures and dynamic behaviors of one and a few molecules. However, further advancement is hindered by lack of large enough yet reproducible enhancement in single deterministic hotspots. To resolve this problem, here we introduce a nanosphere-plane antenna under radially polarized laser excitation experiment, which provides an electromagnetic enhancement of 109~10 at the gap of each individual nanosphere-plane antenna and a root-mean-square error down to 100.08 between them. The experiment also reveals a nonlinear SERS behavior with less than one plasmon, which is also observed within a single hotspot. The unprecedented simultaneous achievement of ultrahigh enhancement and reproducibility in deterministic individual hotspots is attributed to the combination of a well-controlled hotspot geometry, the efficient coupling between vertical antenna and laser which produces orders of magnitude higher enhancement than previous excitation methods, and low power operation which is critical for high reproducibility. Our method opens a path for systematic studies on single and few molecule SERS and their surface chemistry in an in-situ and well-controlled manner.
Improving the performance of the PLB index for ligand-binding site prediction using dihedral angles and the solvent-accessible surface area
Authors: Cao Chen , Xu Shutan
Published: September 2016

Protein ligand-binding site prediction is highly important for protein function determination and structure-based drug design. Over the past twenty years, dozens of computational methods have been developed to address this problem. Soga et al. identified ligand cavities based on the preferences of amino acids for the ligand-binding site (RA) and proposed the propensity for ligand binding (PLB) index to rank the cavities on the protein surface. However, we found that residues exhibit different RAs in response to changes in solvent exposure. Furthermore, previous studies have suggested that some dihedral angles of amino acids in specific regions of the Ramachandran plot are preferred at the functional sites of proteins. Based on these discoveries, the amino acid solvent-accessible surface area and dihedral angles were combined with the RA and PLB to obtain two new indexes, multi-factor RA (MF-RA) and multi-factor PLB (MF-PLB). MF-PLB, PLB and other methods were tested using two benchmark databases and two particular ligand-binding sites. The results show that MF-PLB can improve the success rate of PLB for both ligand-bound and ligand-unbound structures, particularly for top choice prediction.
Sub-CMC solubilization of dodecane by rhamnolipid in saturated porous media
Authors: Zhong Hua , Zhang Hui , Liu Zhifeng , Yang Xin , Brusseau Mark L. , Zeng Guangming
Published: September 2016

Experiments were conducted with a two-dimensional flow cell to examine the effect of monorhamnolipid surfactant at sub-CMC concentrations on solubilization of dodecane in porous media under dynamic flow conditions. Quartz sand was used as the porous medium and artificial groundwater was used as the background solution. The effectiveness of the monorhamnolipid was compared to that of SDBS, Triton X-100, and ethanol. The results demonstrated the enhancement of dodecane solubility by monorhamnolipid surfactant at concentrations lower than CMC. The concentrations (50–210 μM) are sufficiently low that they do not cause mobilization of the dodecane. Retention of rhamnolipid in the porous medium and detection of nano-size aggregates in the effluent show that the solubilization is based on a sub-CMC aggregate-formation mechanism, which is significantly stronger than the solubilization caused by the co-solvent effect. The rhamnolipid biosurfactant is more efficient for the solubilization compared to the synthetic surfactants. These results indicate a strategy of employing low concentrations of rhamnolipid for surfactant-enhanced aquifer remediation (SEAR), which may overcome the drawbacks of using surfactants at hyper-CMC concentrations.
A polymorphic (GA/CT)n- SSR influences promoter activity of Tryptophan decarboxylase gene in Catharanthus roseus L. Don
Authors: Kumar Santosh , Bhatia Sabhyata
Published: September 2016

Simple Sequence Repeats (SSRs) of polypurine-polypyrimidine type motifs occur very frequently in the 5′ flanks of genes in plants and have recently been implicated to have a role in regulation of gene expression. In this study, 2 accessions of Catharanthus roseus having (CT)8 and (CT)21 varying motifs in the 5′UTR of Tryptophan decarboxylase (Tdc) gene, were investigated for its role in regulation of gene expression. Extensive Tdc gene expression analysis in the 2 accessions was carried out both at the level of transcription and translation. Transcript abundance was estimated using Northern analysis and qRT-PCR, whereas the rate of Tdc gene transcription was assessed using in-situ nuclear run-on transcription assay. Translation status of Tdc gene was monitored by quantification of polysome associated Tdc mRNA using qRT-PCR. These observations were validated through transient expression analysis using the fusion construct [CaM35S:(CT)8–21:GUS]. Our study demonstrated that not only does the length of (CT)n -SSRs influences the promoter activity, but the presence of SSRs per se in the 5′-UTR significantly enhances the level of gene expression. We termed this phenomenon as “microsatellite mediated enhancement” (MME) of gene expression. Results presented here will provide leads for engineering plants with enhanced amounts of medicinally important alkaloids.
Optimized holographic femtosecond laser patterning method towards rapid integration of high-quality functional devices in microchannels
Authors: Zhang Chenchu , Hu Yanlei , Du Wenqiang , Wu Peichao , Rao Shenglong , Cai Ze , Lao Zhaoxin , Xu Bing , Ni Jincheng , Li Jiawen , Zhao Gang , Wu Dong , Chu Jiaru , Sugioka Koji
Published: September 2016

Rapid integration of high-quality functional devices in microchannels is in highly demand for miniature lab-on-a-chip applications. This paper demonstrates the embellishment of existing microfluidic devices with integrated micropatterns via femtosecond laser MRAF-based holographic patterning (MHP) microfabrication, which proves two-photon polymerization (TPP) based on spatial light modulator (SLM) to be a rapid and powerful technology for chip functionalization. Optimized mixed region amplitude freedom (MRAF) algorithm has been used to generate high-quality shaped focus field. Base on the optimized parameters, a single-exposure approach is developed to fabricate 200 × 200 μm microstructure arrays in less than 240 ms. Moreover, microtraps, QR code and letters are integrated into a microdevice by the advanced method for particles capture and device identification. These results indicate that such a holographic laser embellishment of microfluidic devices is simple, flexible and easy to access, which has great potential in lab-on-a-chip applications of biological culture, chemical analyses and optofluidic devices.
Voluntary movement affects simultaneous perception of auditory and tactile stimuli presented to a non-moving body part
Authors: Hao Qiao , Ora Hiroki , Ogawa Ken-ichiro , Ogata Taiki , Miyake Yoshihiro
Published: September 2016

The simultaneous perception of multimodal sensory information has a crucial role for effective reactions to the external environment. Voluntary movements are known to occasionally affect simultaneous perception of auditory and tactile stimuli presented to the moving body part. However, little is known about spatial limits on the effect of voluntary movements on simultaneous perception, especially when tactile stimuli are presented to a non-moving body part. We examined the effect of voluntary movement on the simultaneous perception of auditory and tactile stimuli presented to the non-moving body part. We considered the possible mechanism using a temporal order judgement task under three experimental conditions: voluntary movement, where participants voluntarily moved their right index finger and judged the temporal order of auditory and tactile stimuli presented to their non-moving left index finger; passive movement; and no movement. During voluntary movement, the auditory stimulus needed to be presented before the tactile stimulus so that they were perceived as occurring simultaneously. This subjective simultaneity differed significantly from the passive movement and no movement conditions. This finding indicates that the effect of voluntary movement on simultaneous perception of auditory and tactile stimuli extends to the non-moving body part.
Metabolic engineering of cottonseed oil biosynthesis pathway via RNA interference
Authors: Xu Zhongping , Li Jingwen , Guo Xiaoping , Jin Shuangxia , Zhang Xianlong
Published: September 2016

Cottonseed oil is recognized as an important oil in food industry for its unique characters: low flavor reversion and the high level of antioxidants (VitaminE) as well as unsaturated fatty acid. However, the cottonseed oil content of cultivated cotton (Gossypium hirsutum) is only around 20%. In this study, we modified the accumulation of oils by the down-regulation of phosphoenolpyruvate carboxylase 1 (GhPEPC1) via RNA interference in transgenic cotton plants. The qRT-PCR and enzyme activity assay revealed that the transcription and expression of GhPEPC1 was dramatically down-regulated in transgenic lines. Consequently, the cottonseed oil content in several transgenic lines showed a significant (P < 0.01) increase (up to 16.7%) without obvious phenotypic changes under filed condition when compared to the control plants. In order to elucidate the molecular mechanism of GhPEPC1 in the regulation of seed oil content, we quantified the expression of the carbon metabolism related genes of transgenic GhPEPC1 RNAi lines by transcriptome analysis. This analysis revealed the decrease of GhPEPC1 expression led to the increase expression of triacylglycerol biosynthesis-related genes, which eventually contributed to the lipid biosynthesis in cotton. This result provides a valuable information for cottonseed oil biosynthesis pathway and shows the potential of creating high cottonseed oil germplasm by RNAi strategy for cotton breeding.
Pits, a protein interacting with Ttk69 and Sin3A, has links to histone deacetylation
Authors: Liaw Gwo-Jen
Published: September 2016

Histone deacetylation plays an important role in transcriptional repression. Previous results showed that the genetic interaction between ttk and rpd3, which encodes a class I histone deacetylase, is required for tll repression. This study investigated the molecular mechanism by which Ttk69 recruits Rpd3. Using yeast two-hybrid screening and datamining, one novel protein was found that weakly interacts with Ttk69 and Sin3A, designated as Protein interacting with Ttk69 and Sin3A (Pits). Pits protein expressed in the early stages of embryos and bound to the region of the tor response element in vivo. Expanded tll expression patterns were observed in embryos lacking maternal pits activity and the expansion was not widened by reducing either maternal ttk or sin3A activity. However, in embryos with simultaneously reduced maternal pits and sin3A activities or maternal pits, sin3A and ttk activities, the proportions of the embryos with expanded tll expression were significantly increased. These results indicate that all three gene activities are involved in tll repression. Level of histone H3 acetylation in the tll proximal region was found to be elevated in embryo with reduced these three gene activities. In conclusion, Ttk69 causes the histone deacetylation-mediated repression of tll via the interaction of Pits and Sin3A.
Evidence that COMT genotype and proline interact on negative-symptom outcomes in schizophrenia and bipolar disorder
Authors: Clelland C L , Drouet V , Rilett K C , Smeed J A , Nadrich R H , Rajparia A , Read L L , Clelland J D
Published: September 2016

Elevated peripheral proline is associated with psychiatric disorders, and there is evidence that proline is a neuromodulator. The proline dehydrogenase (PRODH) gene, which encodes the enzyme that catalyzes proline catabolism, maps to human chromosome 22q11.2, a region conferring risk of schizophrenia. In the Prodh-null mouse, an interaction between elevated peripheral proline and another 22q11.2 gene, catechol-O-methyltransferase (COMT), on neurotransmission and behavior has been reported. We explored the relationship between fasting plasma proline levels and COMT Val158Met genotype on symptoms (positive, negative and total) in schizophrenia patients. In an exploratory study we also examined symptom change in patients with bipolar disorder. There was a significant interaction between peripheral proline and COMT on negative symptoms in schizophrenia (P<0.0001, n=95). In COMT Val/Val patients, high proline was associated with low Scale for the Assessment of Negative Symptom (SANS) scores. In contrast, high proline was associated with high SANS scores in patients carrying a Met allele. The relationship between proline and COMT also appears to modify negative symptoms across psychiatric illness. In bipolar disorder, a significant interaction was also observed on negative-symptom change (P=0.007, n=43). Negative symptoms are intractable and largely unaddressed by current medications. These data indicate a significant interaction between peripheral proline and COMT genotype, influencing negative symptoms in schizophrenia and bipolar disorder. That high proline has converse effects on symptoms by COMT genotype, may have implications for therapeutic decisions.