bluuebunny/crossref_metadata_2025 huggingface dataset:
Characterization of microfluidic shear-dependent epithelial cell adhesion molecule immunocapture and enrichment of pancreatic cancer cells from blood cells with dielectrophoresis
Authors: Huang Chao , Smith James P. , Saha Trisha N. , Rhim Andrew D. , Kirby Brian J.
Published: July 2014

Current microfluidic techniques for isolating circulating tumor cells (CTCs) from cancer patient blood are limited by low capture purity, and dielectrophoresis (DEP) has the potential to complement existing immunocapture techniques to improve capture performance. We present a hybrid DEP and immunocapture Hele-Shaw flow cell to characterize DEP's effects on immunocapture of pancreatic cancer cells (Capan-1, PANC-1, and BxPC-3) and peripheral blood mononuclear cells (PBMCs) with an anti-EpCAM (epithelial cell adhesion molecule) antibody. By carefully specifying the applied electric field frequency, we demonstrate that pancreatic cancer cells are attracted to immunocapture surfaces by positive DEP whereas PBMCs are repelled by negative DEP. Using an exponential capture model to interpret our capture data, we show that immunocapture performance is dependent on the applied DEP force sign and magnitude, cell surface EpCAM expression level, and shear stress experienced by cells flowing in the capture device. Our work suggests that DEP can not only repel contaminating blood cells but also enhance capture of cancer cell populations that are less likely to be captured by traditional immunocapture methods. This combination of DEP and immunocapture techniques to potentially increase CTC capture purity can facilitate subsequent biological analyses of captured CTCs and research on cancer metastasis and drug therapies.
Band structure mapping of bilayer graphene via quasiparticle scattering
Authors: Yankowitz Matthew , Wang Joel I-Jan , Li Suchun , Birdwell A. Glen , Chen Yu-An , Watanabe Kenji , Taniguchi Takashi , Quek Su Ying , Jarillo-Herrero Pablo , LeRoy Brian J.
Published: July 2014

A perpendicular electric field breaks the layer symmetry of Bernal-stacked bilayer graphene, resulting in the opening of a band gap and a modification of the effective mass of the charge carriers. Using scanning tunneling microscopy and spectroscopy, we examine standing waves in the local density of states of bilayer graphene formed by scattering from a bilayer/trilayer boundary. The quasiparticle interference properties are controlled by the bilayer graphene band structure, allowing a direct local probe of the evolution of the band structure of bilayer graphene as a function of electric field. We extract the Slonczewski-Weiss-McClure model tight binding parameters as γ0 = 3.1 eV, γ1 = 0.39 eV, and γ4 = 0.22 eV.
Model of the magnetization of nanocrystalline materials at low temperatures
Authors: Bian Q. , Niewczas M.
Published: July 2014

A theoretical model incorporating the material texture has been developed to simulate the magnetic properties of nanocrystalline materials at low temperatures where the effect of thermal energy on magnetization is neglected. The method is based on Landau-Lifshitz-Gilbert (LLG) theory and it describes the magnetization dynamics of individual grains in the effective field. The modified LLG equation incorporates the intrinsic fields from the intragrain magnetocrystalline and grain boundary anisotropies and the interacting fields from intergrain dipolar and exchange couplings between the neighbouring grains. The model is applied to study magnetic properties of textured nanocrystalline Ni samples at 2K and is capable to reproduce closely the hysteresis loop behaviour at different orientations of applied magnetic field. Nanocrystalline Ni shows the grain boundary anisotropy constant K1s=−6.0×104J/m3 and the intergrain exchange coupling denoted by the effective exchange constant Ap = 2.16 × 10–11 J/m. Analytical expressions to estimate the intergrain exchange energy density and the effective exchange constant have been formulated.
Dynamics of water in prussian blue analogues: Neutron scattering study
Authors: Sharma V. K. , Mitra S. , Thakur N. , Yusuf S. M. , Juranyi Fanni , Mukhopadhyay R.
Published: July 2014

Dynamics of crystal water in Prussian blue (PB), Fe(III)4[Fe(II)(CN)6]3.14H2O and its analogue Prussian green (PG), ferriferricynaide, Fe(III)4[Fe(III)(CN)6]4.16H2O have been investigated using Quasielastic Neutron Scattering (QENS) technique. PB and its analogue compounds are important materials for their various interesting multifunctional properties. It is known that crystal water plays a crucial role towards the multifunctional properties of Prussian blue analogue compounds. Three structurally distinguishable water molecules: (i) coordinated water molecules at empty nitrogen sites, (ii) non-coordinated water molecules in the spherical cavities, and (iii) at interstitial sites exist in PB. Here spherical cavities are created due to the vacant sites of Fe(CN)6 units. However, PG does not have any such vacant N or Fe(CN)6 units, and only one kind of water molecules, exists only at interstitial sites. QENS experiments have been carried out on both the compounds in the temperature range of 260–360 K to elucidate the dynamical behavior of different kinds of water molecules. Dynamics is found to be much more pronounced in case of PB, compared to PG. A detailed data analysis showed that localized translational diffusion model could describe the observed data for both PB and PG systems. The average diffusion coefficient is found to be much larger in the PB than PG. The obtained domain of dynamics is found to be consistent with the geometry of the structure of the two systems. Combining the data of the two systems, a quantitative estimate of the dynamics, corresponding to the water molecules at different locations is made.
Evidence of Mie scattering at terahertz frequencies in powder materials
Authors: Garet Frédéric , Hofman Maxence , Meilhan Jérôme , Simoens François , Coutaz Jean-Louis
Published: July 2014

We present experimental results as well as modelling concerning terahertz (THz) wave scattering by powder materials with grain size of the order of the wavelength. The studied material is a mixture of high density polyethylene and fructose powders, whose grain size is varied from a sample to another one while the volume concentration is kept constant. Experimental data are recorded with a THz time-domain spectroscopy set up. The scattering contribution to the total propagation loss in such powders shows a resonant behaviour for grain size roughly equal to the THz wavelength, for which it reaches 80%–90% of the total loss. Modelling using Mie theory allows us to well describe the absorption and scattering phenomena.
Electronic passivation of silicon surfaces by thin films of atomic layer deposited gallium oxide
Authors: Allen T. G. , Cuevas A.
Published: July 2014

This paper proposes the application of gallium oxide (Ga2O3) thin films to crystalline silicon solar cells. Effective passivation of n- and p-type crystalline silicon surfaces has been achieved by the application of very thin Ga2O3 films prepared by atomic layer deposition using trimethylgallium (TMGa) and ozone (O3) as the reactants. Surface recombination velocities as low as 6.1 cm/s have been recorded with films less than 4.5 nm thick. A range of deposition parameters has been explored, with growth rates of approximately 0.2 Å/cycle providing optimum passivation. The thermal activation energy for passivation of the Si-Ga2O3 interface has been found to be approximately 0.5 eV. Depassivation of the interface was observed for prolonged annealing at increased temperatures. The activation energy for depassivation was measured to be 1.9 eV.
Bifurcation and chaos in the simple passive dynamic walking model with upper body
Authors: Li Qingdu , Guo Jianli , Yang Xiao-Song
Published: July 2014

We present some rich new complex gaits in the simple walking model with upper body by Wisse et al. in [Robotica 22, 681 (2004)]. We first show that the stable gait found by Wisse et al. may become chaotic via period-doubling bifurcations. Such period-doubling routes to chaos exist for all parameters, such as foot mass, upper body mass, body length, hip spring stiffness, and slope angle. Then, we report three new gaits with period 3, 4, and 6; for each gait, there is also a period-doubling route to chaos. Finally, we show a practical method for finding a topological horseshoe in 3D Poincaré map, and present a rigorous verification of chaos from these gaits.
Self-organization of a periodic structure between amorphous and crystalline phases in a GeTe thin film induced by femtosecond laser pulse amorphization
Authors: Katsumata Y. , Morita T. , Morimoto Y. , Shintani T. , Saiki T.
Published: July 2014

A self-organized fringe pattern in a single amorphous mark of a GeTe thin film was formed by multiple femtosecond pulse amorphization. Micro Raman measurement indicates that the fringe is a periodic alternation between crystalline and amorphous phases. The period of the fringe is smaller than the irradiation wavelength and the direction is parallel to the polarization direction. Snapshot observation revealed that the fringe pattern manifests itself via a complex but coherent process, which is attributed to crystallization properties unique to a nonthermally amorphized phase and the distinct optical contrast between crystalline and amorphous phases.
Molecular beam epitaxial growth of a three-dimensional topological Dirac semimetal Na3Bi
Authors: Zhang Yi , Liu Zhongkai , Zhou Bo , Kim Yeongkwan , Hussain Zahid , Shen Zhi-Xun , Chen Yulin , Mo Sung-Kwan
Published: July 2014

We report a molecular beam epitaxial growth of Na3Bi single-crystal thin films on two different substrates—epitaxial bilayer graphene terminated 6H-SiC(0001) and Si(111). Using reflection high-energy electron diffraction, we found that the lattice orientation of the grown Na3Bi thin film was rotated by 30° respect to the surface lattice orientations of these two substrates. An in-situ angle-resolved photoemission spectroscopy clearly revealed the 3-dimensional Dirac-cone band structure in such thin films. Our approach of growing Na3Bi thin film provides a potential route for further studying its intriguing electronic properties and for fabricating it into practical devices in future.
Failure mechanism analysis and process improvement on time-dependent dielectric breakdown of Cu/ultra-low-k dielectric based on complementary Raman and FTIR spectroscopy study
Authors: Wang Dan Dan , Wang Wei Lin , Huang Maggie Yamin , Lek Alan , Lam Jeffrey , Mai Zhi Hong
Published: July 2014

Time-dependent dielectric breakdown (TDDB) is one of the most important reliability issues in Cu/low-k technology development. With continuous technology scalings to nanometer scales, TDDB issue is further exacerbated. In this paper, two failure mechanisms were investigated: the Ta ions migration model and the line-edge-roughness (LER) model, which is rendering the observed TDDB failure. Complimentary Raman and FTIR spectroscopy was applied to investigate the dielectric bonding characteristics. Our experimental results revealed the TDDB degradation behavior of Cu/ultra-low-k interconnects, suggesting the intrinsic degradation of the ultra-low-k dielectric. No out-diffusion of Cu ions was observed in Cu/Ta/TaN/SiCOH structures. Extensive TEM analysis further verified the migration of Ta ions from the Ta/TaN barrier bi-layer into the ultra-low-k dielectrics. Based on the LER model analysis, a comparative study in both passing and failing die elaborates that the sloped trench/via profile affected the TDDB performance.
Highly sensitive real-time detection of DNA hybridization by using nanoporous waveguide fluorescence spectroscopy
Authors: Fan Yong , Hotta Kazuhiro , Yamaguchi Akira , Ding Yu , He Yonghong , Teramae Norio , Sun Shuqing , Ma Hui
Published: July 2014

In this Letter, we report highly sensitive fluorescence spectroscopy using a nanoporous waveguide (NPWG) comprising a porous anodic alumina (PAA) layer and an Al layer. Simulations show that the TE0 waveguide mode excited in the PAA layer produces an electromagnetic field whose intensity is 40-fold higher than that of the incident light, and which yields enhanced intensity when used to excite fluorophores. We demonstrate the sensing ability of the NPWG by incorporating it into a fluorescent sensor to monitor duplex DNA formation in real-time, with a detection limit as low as 20 pM.
Effect and kinetic mechanism of ultrasonic vibration on solidification of 7050 aluminum alloy
Authors: Jiang Ripeng , Li Xiaoqian , Chen Pinghu , Li Ruiqing , Zhang Xue
Published: July 2014

The work described in this paper dealt with the effect of ultrasonic vibration on the solidification of 7050 aluminum alloy. Two experiments were carried out through introducing ultrasound into the semi-continuous direct-chill (DC) casting of aluminum alloy and into alloy solidifying in a crucible, respectively. Results show that ultrasonic vibration can refine grains in the whole cross-section of a billet in the first experiment and is able to increase the cooling rate within the temperature range from 625 °C to 590 °C in the other one. The mechanism of particle resonance caused by ultrasonic vibration was illustrated on the basis of theoretical analysis of the kinetics and energy conversion during the solidification. It is demonstrated that the kinetic energy of resonant particles are mainly from the latent heat energy of solidification, which can shorten the cooling time, inhibit the crystal growth and then lead to the grain refinement.
A chitosan coated monolith for nucleic acid capture in a thermoplastic microfluidic chip
Authors: Kendall Eric L. , Wienhold Erik , DeVoe Don L.
Published: July 2014

A technique for microfluidic, pH modulated DNA capture and purification using chitosan functionalized glycidyl methacrylate monoliths is presented. Highly porous polymer monoliths are formed and subsequently functionalized off-chip in a batch process before insertion into thermoplastic microchannels prior to solvent bonding, simplifying the overall fabrication process by eliminating the need for on-chip surface modifications. The monolith anchoring method allows for the use of large cross-section monoliths enabling high flowrates and high DNA capture capacity with a minimum of added design complexity. Using monolith capture elements requiring less than 1 mm2 of chip surface area, loading levels above 100 ng are demonstrated, with DNA capture and elution efficiency of 54.2% ± 14.2% achieved.
Genomics-assisted breeding for drought tolerance in chickpea
Authors: Thudi Mahendar , Gaur Pooran M. , Krishnamurthy Lakshmanan , Mir Reyazul R. , Kudapa Himabindu , Fikre Asnake , Kimurto Paul , Tripathi Shailesh , Soren Khela R. , Mulwa Richard , Bharadwaj Chellapilla , Datta Subhojit , Chaturvedi Sushil K. , Varshney Rajeev K.
Published: July 2014

Terminal drought is one of the major constraints in chickpea (Cicer arietinum L.), causing more than 50% production losses. With the objective of accelerating genetic understanding and crop improvement through genomics-assisted breeding, a draft genome sequence has been assembled for the CDC Frontier variety. In this context, 544.73 Mb of sequence data were assembled, capturing of 73.8% of the genome in scaffolds. In addition, large-scale genomic resources including several thousand simple sequence repeats and several million single nucleotide polymorphisms, high-density diversity array technology (15 360 clones) and Illumina GoldenGate assay genotyping platforms, high-density genetic maps and transcriptome assemblies have been developed. In parallel, by using linkage mapping approach, one genomic region harbouring quantitative trait loci for several drought tolerance traits has been identified and successfully introgressed in three leading chickpea varieties (e.g. JG 11, Chefe, KAK 2) by using a marker-assisted backcrossing approach. A multilocation evaluation of these marker-assisted backcrossing lines provided several lines with 10–24% higher yield than the respective recurrent parents.Modern breeding approaches like marker-assisted recurrent selection and genomic selection are being deployed for enhancing drought tolerance in chickpea. Some novel mapping populations such as multiparent advanced generation intercross and nested association mapping populations are also being developed for trait mapping at higher resolution, as well as for enhancing the genetic base of chickpea. Such advances in genomics and genomics-assisted breeding will accelerate precision and efficiency in breeding for stress tolerance in chickpea.
Early detection of Psa infection in kiwifruit by means of infrared thermography at leaf and orchard scale
Authors: Maes Wouter H. , Minchin Peter E. H. , Snelgar William P. , Steppe Kathy
Published: July 2014

Pseudomonas syringae pv. actinidiae (Psa), the causal agent of bacterial canker of kiwifruit, has become a worldwide threat for the kiwifruit industry. In this work, the potential of infrared thermography for early detection of physiological symptoms related to Psa-infection at leaf and at orchard block scale was assessed. At the leaf level, thermal cold spots appeared shortly after Psa-infection, well before any visual symptoms. A few weeks after infection, thermal hot spots were observed, associated with, but not limited to, spots of visible leaf necrosis. At orchard block level, Psa-infected canes were significantly warmer in both blocks and on all measurement days. A novel wet reference surface, existing of a cluster of cotton imitation leaves with similar dimensions and orientation as real leaves and remaining wet through sucking up water from a small container, was used to estimate the crop water stress index (CWSI). CWSI showed stable values of infected and uninfected areas during the day and between following days. Crop temperature and CWSI were closely correlated with leaf stomatal conductance, which was lower in infected canes. A Psa-infection map based on canopy temperature revealed that Psa infects the outer canes rather than the central part of the canopy.
Exploring exoplanet populations with NASA’s Kepler Mission
Authors: Batalha Natalie M.
Published: July 2014

The Kepler Mission is exploring the diversity of planets and planetary systems. Its legacy will be a catalog of discoveries sufficient for computing planet occurrence rates as a function of size, orbital period, star type, and insolation flux. The mission has made significant progress toward achieving that goal. Over 3,500 transiting exoplanets have been identified from the analysis of the first 3 y of data, 100 planets of which are in the habitable zone. The catalog has a high reliability rate (85–90% averaged over the period/radius plane), which is improving as follow-up observations continue. Dynamical (e.g., velocimetry and transit timing) and statistical methods have confirmed and characterized hundreds of planets over a large range of sizes and compositions for both single- and multiple-star systems. Population studies suggest that planets abound in our galaxy and that small planets are particularly frequent. Here, I report on the progress
Kepler
has made measuring the prevalence of exoplanets orbiting within one astronomical unit of their host stars in support of the National Aeronautics and Space Administration’s long-term goal of finding habitable environments beyond the solar system.
Predicting fruit fly’s sensing rate with insect flight simulations
Authors: Chang Song , Wang Z. Jane
Published: July 2014

Significance

To balance in air, insects not only need to generate enough lift, but also have to make subtle adjustments to their wing movement to stabilize themselves. The tiny changes during complex wing movement, together with the intricacy of the underlying neural feedback system, make it extremely difficult to observe the key changes and to tease out the internal control algorithms insects use to stabilize themselves. With computational simulations and analyses, we can now make predictions about how fast and how frequently a model insect must sense and act to stabilize itself. Our results offer a strategy for effective stabilization of flapping flight and lead us to conjecture that fruit flies sense their kinematic state every wing beat.
Phosphatidylinositol 4,5-bisphosphate triggers activation of focal adhesion kinase by inducing clustering and conformational changes
Authors: Goñi Guillermina M. , Epifano Carolina , Boskovic Jasminka , Camacho-Artacho Marta , Zhou Jing , Bronowska Agnieszka , Martín M. Teresa , Eck Michael J. , Kremer Leonor , Gräter Frauke , Gervasio Francesco Luigi , Perez-Moreno Mirna , Lietha Daniel
Published: July 2014

Significance

Nonreceptor tyrosine kinases are major players in cell signaling. Among them, focal adhesion kinase (FAK) is the key integrator of signals from growth factors and cell adhesion. In cancer, FAK is frequently overexpressed, and by promoting adhesion to the tumor stroma and ECM, FAK provides important signals for tumor invasion and metastasis. Although autoinhibitory mechanisms have previously been described and the players involved in FAK regulation are largely known, on a mechanistic level, FAK activation is currently not understood. Here, we present a multidisciplinary approach demonstrating a multistep mechanism resulting in FAK activation. This mechanistic insight enables the design of alternative strategies for the discovery of potential anticancer drugs that inhibit both catalytic and scaffolding functions of FAK with high specificity.
PAPD5-mediated 3′ adenylation and subsequent degradation of miR-21 is disrupted in proliferative disease
Authors: Boele Joost , Persson Helena , Shin Jay W. , Ishizu Yuri , Newie Inga S. , Søkilde Rolf , Hawkins Shannon M. , Coarfa Cristian , Ikeda Kazuhiro , Takayama Ken-ichi , Horie-Inoue Kuniko , Ando Yoshinari , Burroughs A. Maxwell , Sasaki Chihiro , Suzuki Chizuru , Sakai Mizuho , Aoki Shintaro , Ogawa Ayumi , Hasegawa Akira , Lizio Marina , Kaida Kaoru , Teusink Bas , Carninci Piero , Suzuki Harukazu , Inoue Satoshi , Gunaratne Preethi H. , Rovira Carlos , Hayashizaki Yoshihide , de Hoon Michiel J. L.
Published: July 2014

Significance

MicroRNAs (miRNAs) are small RNAs that regulate genes by selectively silencing their target messenger RNAs. They are often produced as various sequence variants that differ at their 3′ or 5′ ends. While 5′ sequence variations affect which messenger RNAs are targeted by the miRNA, the functional significance of 3′ sequence variants remains largely elusive. Here, we analyze 3′ sequence variants of miR-21, a miRNA well known for its crucial role in cancer and other diseases. We show that tumor suppressor PAPD5 mediates adenosine addition to the 3′ end of miR-21, followed by its 3′-to-5′ trimming by an exoribonuclease. We find that this degradation pathway is disrupted across a wide variety of cancers, highlighting its importance in human disease.
Synthesis of bioactive protein hydrogels by genetically encoded SpyTag-SpyCatcher chemistry
Authors: Sun Fei , Zhang Wen-Bin , Mahdavi Alborz , Arnold Frances H. , Tirrell David A.
Published: July 2014

Significance

Advances in tissue engineering and regenerative medicine have created a need for new biomaterial scaffolds that facilitate cell encapsulation and transplantation. Here we present an approach to the synthesis of artificial protein scaffolds that form spontaneously under physiological conditions. These protein hydrogels may be designed to include cell-adhesion ligands, protease cleavage sites, and full-length globular proteins that carry the information needed to program the behavior of encapsulated cells. We demonstrate the approach by encapsulating mouse embryonic stem cells in a protein scaffold that includes leukemia inhibitory factor (LIF); the encapsulated cells remain pluripotent in the absence of added LIF. The results presented here illustrate a versatile strategy for the creation of information-rich biomaterials.
Subpolar addition of new cell wall is directed by DivIVA in mycobacteria
Authors: Meniche Xavier , Otten Renee , Siegrist M. Sloan , Baer Christina E. , Murphy Kenan C. , Bertozzi Carolyn R. , Sassetti Christopher M.
Published: July 2014

Significance

The tropomyosin-like protein, DivIVA, determines the site of growth and cell morphology in mycobacteria. Surprisingly, although DivIVA is located at the tip of the growing cell pole, cell wall addition is excluded from this site. Both late cell wall synthetic enzymes and new cell wall deposition occur at a subpolar space, distinct from the DivIVA-marked cell tip. Instead of directly recruiting terminal cell wall synthetic systems, DivIVA interacts with enzymes involved in the early steps of the cell wall precursor synthesis. These results suggest a unique organization of the polar elongasome, where cell wall precursors are concentrated at the cell tip by DivIVA and then incorporated into the nascent cell wall in an annular pattern at the subpolar zone.
A phage protein that inhibits the bacterial ATPase required for type IV pilus assembly
Authors: Chung In-Young , Jang Hye-Jeong , Bae Hee-Won , Cho You-Hee
Published: July 2014

Significance

We have identified a phage-encoded protein that inhibits the bacterial ATPase PilB, which is involved in type IV pilus (TFP) biogenesis and function. This phage protein-mediated PilB dysfunction is regarded as the superinfection-exclusion maneuver of the phage toward TFP-specific phages. This study inspires an antipathogenic target based on the ATPases ubiquitously conserved in the motility and secretion machineries important in bacterial pathogenesis.
Lysine methylation-dependent binding of 53BP1 to the pRb tumor suppressor
Authors: Carr Simon M. , Munro Shonagh , Zalmas Lykourgos-Panagiotis , Fedorov Oleg , Johansson Catrine , Krojer Tobias , Sagum Cari A. , Bedford Mark T. , Oppermann Udo , La Thangue Nicholas B.
Published: July 2014

Significance

The retinoblastoma protein (pRb) is a key regulator of cell cycle progression and the DNA damage response. Its importance in these processes is highlighted by the fact that it is mutated or functionally inactivated in almost all human tumors. Its activity is finely regulated by a number of post-translational modifications, including phosphorylation and methylation, which act to recruit “reader” proteins that mediate signaling events. Here, to our knowledge for the first time, we describe the methyl-dependent interaction between pRb and the tudor domain containing tumor protein p53 binding protein 1 (53BP1) and describe how this interaction integrates pRb cell cycle control with the DNA damage response. Our results therefore widen the repertoire of cellular targets for 53BP1 and suggest a new role in regulating pRb tumor suppressor activity.
Complete genome of a nonphotosynthetic cyanobacterium in a diatom reveals recent adaptations to an intracellular lifestyle
Authors: Nakayama Takuro , Kamikawa Ryoma , Tanifuji Goro , Kashiyama Yuichiro , Ohkouchi Naohiko , Archibald John M. , Inagaki Yuji
Published: July 2014

Significance

Members of the diatom family Rhopalodiaceae possess a cyanobacterial endosymbiont called a “spheroid body.” The spheroid body evolved much more recently than did mitochondria or plastids and is predicted to fix nitrogen. Here we present what is, to our knowledge, the first completely sequenced spheroid body genome from a rhopalodiacean diatom. Comparative analyses revealed that the endosymbiont is metabolically reduced, confirming its status as an obligate endosymbiont. The genome possesses genes for nitrogen fixation, and, to our surprise, no essential genes for photosynthesis. Thus, the spheroid body is, to our knowledge, the first known example of a nonphotosynthetic cyanobacterium, free-living or symbiotic. Rhopalodiacean diatoms have the potential to provide unique insight into the evolution of bacterial endosymbionts and their hosts.
Secondary bacterial flagellar system improves bacterial spreading by increasing the directional persistence of swimming
Authors: Bubendorfer Sebastian , Koltai Mihaly , Rossmann Florian , Sourjik Victor , Thormann Kai M.
Published: July 2014

Significance

Flagella-mediated motility is an important or even crucial propagation factor for many bacteria. A number of polarly flagellated species possess a distinct secondary flagellar system, which, as current models suggest, allows more effective swimming under conditions of elevated viscosity or across surfaces. In this study, we demonstrate that such a secondary flagellar system may also exert beneficial effects in bacterial spreading by increasing the directional persistence through lowering the cellular turning angles. The strategy of increasing directional persistence to improve animal spreading efficiency has been proposed previously by theoretical modeling, and here we provide a specific example of how this strategy is used by bacteria.
Dissecting allosteric effects of activator–coactivator complexes using a covalent small molecule ligand
Authors: Wang Ningkun , Lodge Jean M. , Fierke Carol A. , Mapp Anna K.
Published: July 2014

Significance

The master coactivator CREB binding protein (CBP)/p300 utilizes several conformationally dynamic protein–protein interaction motifs to regulate the transcriptional status of essential genes. The kinase-inducible domain interacting (KIX) domain within CBP/p300 forms complexes with multiple transcriptional activators, using two allosterically connected binding surfaces. Here transient kinetic experiments of KIX–ligand complexes were used to dissect the underlying mechanism of the allosteric alterations in ternary complex formation. For positive cooperativity, the stabilization of protein–ligand complex as indicated by a decrease in
k
off
is the primary determinant. In contrast, negative cooperativity was derived by a decrease in
k
on
and an increase in
k
off
. As KIX–activator complexes are important models for intrinsically disordered protein complexes, these data provide a broader mechanistic framework for positive and negative cooperativity.
Improving fatty acids production by engineering dynamic pathway regulation and metabolic control
Authors: Xu Peng , Li Lingyun , Zhang Fuming , Stephanopoulos Gregory , Koffas Mattheos
Published: July 2014

Significance

One important synthetic chemistry reaction endowed by nature is the decarboxylative carbon condensation reaction using malonyl-CoA as carbon donor. Previous metabolic engineering efforts centered on the malonyl-CoA–dependent pathway have resulted in the production of many value-added compounds. Here we mimicked the native biological systems and used a dynamic regulatory network to optimize production titers and yield. The naturally existing transcriptional regulator FapR was rewired to dynamically control gene expressions involved in the supply and consumption of malonyl-CoA. Applying this metabolic control allowed the engineered cell to dynamically regulate pathway expression and compensated the metabolic activity of critical enzymes. The synthetic malonyl-CoA switch engineered in this study opens up new venues for dynamic pathway optimization and efficient production of malonyl-CoA–derived compounds.
Energy conservation by oxidation of formate to carbon dioxide and hydrogen via a sodium ion current in a hyperthermophilic archaeon
Authors: Lim Jae Kyu , Mayer Florian , Kang Sung Gyun , Müller Volker
Published: July 2014

Significance

We report here that oxidation of formate to CO
2
and H
2
that operates close to thermodynamic equilibrium is coupled to vectorial H
+
and Na
+
transport across the cytoplasmic membrane of the hyperthermophilic archaeon
Thermococcus onnurineus
NA1. The ion gradient established then drives ATP synthesis via a Na
+
-ATP synthase. The energy-converting enzyme complex involves a formate dehydrogenase, a membrane-bound hydrogenase with similarity to complex I of the aerobic electron transport chain and a multisubunit Na
+
/H
+
antiporter.
Type-I interferon signaling through ISGF3 complex is required for sustained Rip3 activation and necroptosis in macrophages
Authors: McComb Scott , Cessford Erin , Alturki Norah A. , Joseph Julie , Shutinoski Bojan , Startek Justyna B. , Gamero Ana M. , Mossman Karen L. , Sad Subash
Published: July 2014

Significance

Although it has long been known that inflammatory immune responses are associated with death of cells through necrosis, the mechanisms controlling this process are not yet well understood. Recently a type of programmed inflammatory cell death, necroptosis, has been discovered. In this paper we reveal previously unidentified molecular mechanisms that operate to induce this form of cell death. Our results indicate that in order to undergo necroptosis, immune cells must produce and receive signals from the key immune regulator, interferon. Such interferon-dependent necroptosis of immune cells drives acute inflammatory pathology in a mouse model of sepsis. This work highlights the intimate connection between cell death and inflammation, and may lead to new understanding and treatment of inflammatory pathologies.
Auxin transport sites are visualized in planta using fluorescent auxin analogs
Authors: Hayashi Ken-ichiro , Nakamura Shouichi , Fukunaga Shiho , Nishimura Takeshi , Jenness Mark K. , Murphy Angus S. , Motose Hiroyasu , Nozaki Hiroshi , Furutani Masahiko , Aoyama Takashi
Published: July 2014

Significance

Fluorescent auxin analogs are designed to function as active auxins for the auxin transport system but to be inactive for auxin signaling. These fluorescent auxin analogs can mimic auxin via the transport system and be used to visualize inter- and intracellular auxin distribution in roots. These analogs allow imaging of auxin transport sites with high spatiotemporal resolution. Our fluorescent auxin system provides insight into auxin transport dynamics and subcellular auxin distribution.
Critical role of canonical transient receptor potential channel 7 in initiation of seizures
Authors: Phelan Kevin D. , Shwe U Thaung , Abramowitz Joel , Birnbaumer Lutz , Zheng Fang
Published: July 2014

Significance

Canonical transient receptor potential (TRPC) channels are a family of polymodal cation channels. TRPC7 was the last member of the TRPC family cloned, and the functional role of TRPC7 in the brain is completely unknown. Here, we show that genetic ablation of TRPC7 disrupts acute severe seizures induced by pilocarpine in mice. This disruption is associated with a reduction in pilocarpine-induced increase in gamma wave activity that precedes the acute seizures. At the cellular level, loss of TRPC7 shows reduced long-term potentiation at cornu ammonis (CA) 3 recurrent collateral synapses, which is critical for the generation of epileptiform burst firing in the CA3 region of the hippocampus. Our findings reveal a critical role for TRPC7 in the generation of seizures.
Blockade of oncogenic IκB kinase activity in diffuse large B-cell lymphoma by bromodomain and extraterminal domain protein inhibitors
Authors: Ceribelli Michele , Kelly Priscilla N. , Shaffer Arthur L. , Wright George W. , Xiao Wenming , Yang Yibin , Mathews Griner Lesley A. , Guha Rajarshi , Shinn Paul , Keller Jonathan M. , Liu Dongbo , Patel Paresma R. , Ferrer Marc , Joshi Shivangi , Nerle Sujata , Sandy Peter , Normant Emmanuel , Thomas Craig J. , Staudt Louis M.
Published: July 2014

Significance

The activated B-cell–like (ABC) subtype of diffuse large B-cell lymphoma (DLBCL) is an aggressive cancer that can only be cured in roughly 40% of cases. These malignant cells rely on the NF-κB signaling pathway for survival. Here, we report that genetic or pharmacologic interference with bromodomain and extraterminal domain (BET) chromatin proteins reduces NF-κB activity and ABC DLBCL viability. Unexpectedly, the mechanism involves inhibition of IκB kinase, the key cytoplasmic enzyme that activates the NF-κB pathway. The NF-κB pathway in ABC DLBCL is activated by B-cell receptor signaling, which can be blocked by the BTK kinase inhibitor ibrutinib. BET inhibitors synergized with ibrutinib to decrease growth of ABC DLBCL tumors in mouse models. BET inhibitors should be evaluated in ABC DLBCL clinical trials.
Characterization and immobilization on nickel-chelated Sepharose of a glutamate decarboxylase A from Lactobacillus brevis BH2 and its application for production of GABA
Authors: Lee Ji-Yeon , Jeon Sung-Jong
Published: July 2014

A gene encoding glutamate decarboxylase A (GadA) from Lactobacillus brevis BH2 was expressed in a His-tagged form in Escherichia coli cells, and recombinant protein exists as a homodimer consisting of identical subunits of 53 kDa. GadA was absolutely dependent on the ammonium sulfate concentration for catalytic activity and secondary structure formation. GadA was immobilized on the metal affinity resin with an immobilization yield of 95.8%. The pH optima of the immobilized enzyme were identical with those of the free enzyme. However, the optimum temperature for immobilized enzyme was 5 °C higher than that for the free enzyme. The immobilized GadA retained its relative activity of 41% after 30 reuses of reaction within 30 days and exhibited a half-life of 19 cycles within 19 days. A packed-bed bioreactor with immobilized GadA showed a maximum yield of 97.8% GABA from 50 mM l-glutamate in a flow-through system under conditions of pH 4.0 and 55 °C.
Enhanced levels of nicotianamine promote iron accumulation and tolerance to calcareous soil in soybean
Authors: Nozoye Tomoko , Kim Suyoen , Kakei Yusuke , Takahashi Michiko , Nakanishi Hiromi , Nishizawa Naoko K
Published: July 2014

Iron (Fe) is an essential nutrient in both plants and humans. Fe deficiency on calcareous soil with low Fe availability is a major agricultural problem. Nicotianamine (NA) is one of the Fe chelator in plants, which is involved in metal translocation into seeds, and serves as an antihypertensive substance in humans. In this study, soybean plants overexpressing the barley NA synthase 1 (HvNAS1) gene driven by the constitutive CaMV 35S promoter were produced using Agrobacterium-mediated transformation. The transgenic soybean showed no growth defect and grew normally. The NA content of transgenic soybean seeds was up to four-fold greater than that of non-transgenic (NT) soybean seeds. The level of HvNAS1 expression was positively correlated with the amount of NA, and a high concentration of NA was maintained in the seeds in succeeding generations. The Fe concentration was approximately two-fold greater in transgenic soybean seeds than in NT soybean seeds. Furthermore, the transgenic soybeans showed tolerance to low Fe availability in calcareous soil. Our results suggested that increasing the NA content in soybean seeds by the overexpression of HvNAS1 offers potential benefits for both human health and agricultural productivity.
De novo assembly, gene annotation, and simple sequence repeat marker development using Illumina paired-end transcriptome sequences in the pearl oyster Pinctada maxima
Authors: Deng Yuewen , Lei Qiannan , Tian Qunli , Xie Shaohe , Du Xiaodong , Li Junhui , Wang Liqun , Xiong Yuanxin
Published: July 2014

We analyzed the mantle transcriptome of pearl oyster Pinctada maxima and developed EST–SSR markers using Illumina HiSeq 2000 paired-end sequencing technology. A total of 49,500,748 raw reads were generated. De novo assembly generated 108,704 unigenes with an average length of 407 bp. Sequence similarity search with known proteins or nucleotides revealed that 30,200 (27.78%) and 25,824 (23.76%) consensus sequences were homologous with the sequences in the non-redundant protein and Swiss–Prot databases, respectively, and that 19,701 (18.12%) of these unigenes were possibly involved in approximately 234 known signaling pathways in the Kyoto Encyclopedia of Genes and Genomes database. Ninety one biomineralization-related unigenes were detected. In a cultured stock, 1764 simple sequence repeats were identified and 56 primer pairs were randomly selected and tested. The rate of successful amplification was 68.3%. The developed molecular markers are helpful for further studies on genetic linkage analysis, gene localization, and quantitative trait loci mapping.
Spatial Associations in Numerical Cognition—From Single Digits to Arithmetic
Authors: Fischer Martin H. , Shaki Samuel
Published: July 2014

The literature on spatial associations during number processing is dominated by the SNARC (spatial–numerical association of response codes) effect. We describe spatial biases found for single digits and pairs of numbers, first in the “original” speeded parity task and then extending the scope to encompass different tasks, a range of measures, and various populations. Then we review theoretical accounts before surveying the emerging evidence for similar spatial associations during mental arithmetic. We conclude that the mental number line hypothesis and an embodied approach are useful frameworks for further studies.
A molecular basis underpinning the T cell receptor heterogeneity of mucosal-associated invariant T cells
Authors: Eckle Sidonia B.G. , Birkinshaw Richard W. , Kostenko Lyudmila , Corbett Alexandra J. , McWilliam Hamish E.G. , Reantragoon Rangsima , Chen Zhenjun , Gherardin Nicholas A. , Beddoe Travis , Liu Ligong , Patel Onisha , Meehan Bronwyn , Fairlie David P. , Villadangos Jose A. , Godfrey Dale I. , Kjer-Nielsen Lars , McCluskey James , Rossjohn Jamie
Published: July 2014

Mucosal-associated invariant T (MAIT) cells express an invariant T cell receptor (TCR) α-chain (TRAV1-2 joined to TRAJ33, TRAJ20, or TRAJ12 in humans), which pairs with an array of TCR β-chains. MAIT TCRs can bind folate- and riboflavin-based metabolites restricted by the major histocompatibility complex (MHC)-related class I−like molecule, MR1. However, the impact of MAIT TCR and MR1-ligand heterogeneity on MAIT cell biology is unclear. We show how a previously uncharacterized MR1 ligand, acetyl-6-formylpterin (Ac-6-FP), markedly stabilized MR1, potently up-regulated MR1 cell surface expression, and inhibited MAIT cell activation. These enhanced properties of Ac-6-FP were attributable to structural alterations in MR1 that subsequently affected MAIT TCR recognition via conformational changes within the complementarity-determining region (CDR) 3β loop. Analysis of seven TRBV6-1+ MAIT TCRs demonstrated how CDR3β hypervariability impacted on MAIT TCR recognition by altering TCR flexibility and contacts with MR1 and the Ag itself. Ternary structures of TRBV6-1, TRBV6-4, and TRBV20+ MAIT TCRs in complex with MR1 bound to a potent riboflavin-based antigen (Ag) showed how variations in TRBV gene usage exclusively impacted on MR1 contacts within a consensus MAIT TCR-MR1 footprint. Moreover, differential TRAJ gene usage was readily accommodated within a conserved MAIT TCR-MR1-Ag docking mode. Collectively, MAIT TCR heterogeneity can fine-tune MR1 recognition in an Ag-dependent manner, thereby modulating MAIT cell recognition.
OsNAC111, a Blast Disease–Responsive Transcription Factor in Rice, Positively Regulates the Expression of Defense-Related Genes
Authors: Yokotani Naoki , Tsuchida-Mayama Tomoko , Ichikawa Hiroaki , Mitsuda Nobutaka , Ohme-Takagi Masaru , Kaku Hisatoshi , Minami Eiichi , Nishizawa Yoko
Published: July 2014

Plants respond to pathogen attack by transcriptionally regulating defense-related genes via various types of transcription factors. We identified a transcription factor in rice, OsNAC111, belonging to the TERN subgroup of the NAC family that was transcriptionally upregulated after rice blast fungus (Magnaporthe oryzae) inoculation. OsNAC111 was localized in the nucleus of rice cells and had transcriptional activation activity in yeast and rice cells. Transgenic rice plants overexpressing OsNAC111 showed increased resistance to the rice blast fungus. In OsNAC111-overexpressing plants, the expression of several defense-related genes, including pathogenesis-related (PR) genes, was constitutively high compared with the control. These genes all showed blast disease-responsive expression in leaves. Among them, two chitinase genes and one β-1,3-glucanase gene showed reduced expression in transgenic rice plants in which OsNAC111 function was suppressed by a chimeric repressor (OsNAC111-SRDX). OsNAC111 activated transcription from the promoters of the chitinase and β-1,3-glucanase genes in rice cells. In addition, brown pigmentation at the infection sites, a defense response of rice cells to the blast fungus, was lowered in OsNAC111-SRDX plants at the early infection stage. These results indicate that OsNAC111 positively regulates the expression of a specific set of PR genes in the disease response and contributes to disease resistance.
Bioguided Isolation, Characterization, and Biotransformation byFusarium verticillioidesof Maize Kernel Compounds That Inhibit Fumonisin Production
Authors: Atanasova-Penichon Vessela , Bernillon Stéphane , Marchegay Gisèle , Lornac Aurélia , Pinson-Gadais Laetitia , Ponts Nadia , Zehraoui Enric , Barreau Christian , Richard-Forget Florence
Published: July 2014

Fusarium verticillioides infects maize ears, causing ear rot disease and contamination of grain with fumonisin mycotoxins. This contamination can be reduced by the presence of bioactive compounds in kernels that are able to inhibit fumonisin biosynthesis. To identify such compounds, we used kernels from a maize genotype with moderate susceptibility to F. verticillioides, harvested at the milk-dough stage (i.e., when fumonisin production initiates in planta), and applied a bioguided fractionation approach. Chlorogenic acid was the most abundant compound in the purified active fraction and its contribution to fumonisin inhibitory activity was up to 70%. Moreover, using a set of maize genotypes with different levels of susceptibility, chlorogenic acid was shown to be significantly higher in immature kernels of the moderately susceptible group. Altogether, our data indicate that chlorogenic acid may considerably contribute to either maize resistance to Fusarium ear rot, fumonisin accumulation, or both. We further investigated the mechanisms involved in the inhibition of fumonisin production by chlorogenic acid and one of its hydrolyzed products, caffeic acid, by following their metabolic fate in supplemented F. verticillioides broths. Our data indicate that F. verticillioides was able to biotransform these phenolic compounds and that the resulting products can contribute to their inhibitory activity.