bluuebunny/crossref_metadata_2025 huggingface dataset:
Engineering of tunnel junctions for prospective spin injection in germanium
Authors: Zhou Yi , Ogawa Masaaki , Bao Mingqiang , Han Wei , Kawakami Roland K. , Wang Kang L.
Published: June 2009

Even though the strong Fermi-level pinning at the metal/germanium (Ge) interface can be alleviated by inserting a thin layer of tunneling oxide, the still sizeable Schottky barriers and the wide depletion regions of the Fe/oxide/n-Ge contacts make the junction resistances strongly dependent of temperature. The resistance-area (RA) products of these junctions are too high for spin injection and cannot be tuned by simply varying oxide thickness or using ferromagnetic metal (FM) with a lower work function. In this work, low energy ion implantation and rapid thermal annealing were utilized to degenerately dope the Ge surface layer to facilitate single-step tunneling transport. The RA products of the junctions with surface doping are significantly reduced and weakly dependent of temperature. This method gives a prospect for spin injection to Ge from FM.
White light-emitting devices based on the combined emission from red CdSe/ZnS quantum dots, green phosphorescent, and blue fluorescent organic molecules
Authors: Cheng Gang , Mazzeo Marco , Rizzo Aurora , Li Yanqin , Duan Yu , Gigli Giuseppe
Published: June 2009

We report on a white hybrid light-emitting device realized by combining red emission from CdSe/ZnS quantum dots (QDs), green emission from a phosphorescent organic complex tris[2-4(4-toltyl)phenylpyridine]iridium [Ir(mppy)3], and blue emission from a fluorescent organic emitter 2,2′,7,7′-tetrakis(2,2-diphenylvinyl)spiro-9,9′-bifluorene. Energy transfer processes from the organic components to the QDs have been analyzed versus the Ir(mppy)3 concentration in order to optimize the device performances. A maximum external quantum efficiency of 2.1%, corresponding to a power efficiency of 2.2 lm/W at 13 mA/cm2, and a color rendering index of 89.8 at 10 200 cd/m2 were achieved.
Hole size dependence of forward emission from organic dyes coated with two-dimensional metallic arrays
Authors: Li J. , Xu J. B. , Ong H. C.
Published: June 2009

The effects of hole size on the forward emission from organic dyes coated with two-dimensional Au hole arrays have been studied by angle-dependent reflectivity and photoluminescence. It is found that when the hole radius increases from 73 to 116 nm, the emission intensity and bandwidth are enhanced by 2.5 and 2 times, respectively. By correlating the photoluminescence and reflectivity mappings, we have attributed the enhancement of emission primarily to the increase in radiation coupling efficiency to surface plasmons and surface plasmon radiative decay rate.
Observation of temperature-independent internal Er3+ relaxation efficiency in Si-rich SiO2 films
Authors: Savchyn Oleksandr , Todi Ravi M. , Coffey Kevin R. , Kik Pieter G.
Published: June 2009

Time-dependent photoluminescence measurements of low-temperature-annealed Er-doped Si-rich SiO2 were conducted at sample temperatures 15–300 K. The erbium internal relaxation efficiency from the second (I411/2) to the first (I413/2) excited state upon luminescence-center-mediated Er3+ excitation is investigated. Despite the observation of temperature-dependent relaxation rates, the erbium internal relaxation efficiency is found to be remarkably temperature independent, which suggests that the internal relaxation efficiency is near unity. Internal relaxation is shown to account for 50%–55% of the I413/2 excitation events in the entire temperature range. These results demonstrate that high pump efficiency and stable operation of devices based on this material will be possible under varying thermal conditions.
Band profiles of ZnMgO/ZnO heterostructures confirmed by Kelvin probe force microscopy
Authors: Tampo H. , Shibata H. , Maejima K. , Chiu T.-W. , Itoh H. , Yamada A. , Matsubara K. , Fons P. , Chiba Y. , Wakamatsu T. , Takeshita Y. , Kanie H. , Niki S.
Published: June 2009

The band profiles of ZnMgO/ZnO heterostructures were confirmed through surface potential measurements by Kelvin probe force microscopy. A simple model for the band profile was proposed and the various band parameters were evaluated experimentally and theoretically based on the band model. The band profile was calculated and validated with experimental results using the Schrödinger–Poisson equation. The energy level of the ZnMgO surface donor state, which serves as the source of the two-dimensional electron gas in ZnMgO/ZnO heterostructures, was estimated from the band parameters; nearly identical energy levels around 0.8 eV were obtained for Zn1−xMgxO layers with Mg compositions x ranging from 0.12 to 0.42 and the corresponding charge densities were estimated to be 8×1012 cm−2.
Effect of solution viscosity on generating long DNA nanostrands array via patterned molecular combing
Authors: Cheng Jun-Jie , Chang Yuan-Hsin , Huang Wan-Yu , Juang Yi-Je
Published: June 2009

In this study, we have investigated the effect of solution viscosity on generating the aligned and long DNA nanostrands array via modified molecular combing/soft lithography technique (or patterned molecular combing). By using the solution with higher viscosity, a low peeling-off speed can be applied to generate the long DNA nanostrands and the thornlike structures can be eliminated effectively. The DNA nanostrands array can also be generated by utilizing the polydimethylsiloxane stamp having microwells with larger diameter; however, variation of the lengths of the DNA nanostrands becomes greater as the solution viscosity and the size of microwells increase.
Strong fields induce ultrafast rearrangement of H atoms in H2O
Authors: Rajgara F. A. , Dharmadhikari A. K. , Mathur D. , Safvan C. P.
Published: June 2009

H atoms in H2O are rearranged by strong optical fields generated by intense 9.3 fs laser pulses to form H2+. This atomic rearrangement is ultrafast: It occurs within a single laser pulse. Quantum-chemical calculations reveal that H2+ originates in the A1 state of H2O2+ when the O–H bond elongates to 1.15 a.u. and the H–O–H angle becomes 120°. Bond formation on the ultrafast time scale of molecular vibrations (10 fs for H2+) and in strong fields has hitherto not been reported.
Transport properties and induced voltage in the structure of water-filled single-walled boron-nitrogen nanotubes
Authors: Yuan Quanzi , Zhao Ya-Pu
Published: June 2009

Density functional theory/molecular dynamics simulations were employed to give insights into the mechanism of voltage generation based on a water-filled single-walled boron-nitrogen nanotube (SWBNNT). Our calculations showed that (1) the transport properties of confined water in a SWBNNT are different from those of bulk water in view of configuration, the diffusion coefficient, the dipole orientation, and the density distribution, and (2) a voltage difference of several millivolts would generate between the two ends of a SWBNNT due to interactions between the water dipole chains and charge carriers in the tube. Therefore, this structure of a water-filled SWBNNT can be a promising candidate for a synthetic nanoscale power cell as well as a practical nanopower harvesting device.
Variations of Value Creation: Automobile Manufacturing in Thailand
Authors: Hassler Markus
Published: June 2009

The increasing integration of the Thai automobile industry into the global economy throughout the last three decades has been influenced by a number of factors. Although the general increase in demand has created the basic precondition for global automobile firms to serve this particular market, the way in which these automobile firms operate in the Thai economy is subject to regulatory frameworks operating at different geographical scales. Indeed, the exercise of institutional power at the national and macroregional scale, regulating automobile production and trade within Thailand and the ASEAN Free Trade Area (AFTA) has a significant impact on the way in which firms embed themselves into, and how value is created within, the Thai economy. However, the network configurations of the lead firms operating in Thailand vary significantly. The way and extent to which lead firms create and enhance value within this national economy are strongly dependent on the manufactured product.
Anger and Happiness are Linked Differently to the Explicit Detection of Biological Motion
Authors: Ikeda Hanako , Watanabe Katsumi
Published: June 2009

The detection of biological motion and the detection of emotion from this motion are important visual functions with obvious survival and social values. The perception of biological motion is remarkably robust, and numerous studies have shown that the emotional states of a person can be deduced from point-light biological motion. In the present study, we investigated the extent to which the detection of emotion from biological motion is linked to the explicit detection of human gait. Subjects performed gait detection and emotion detection for the same stimulus. The stimulus consisted of one coherent interval and one scrambled biological-motion interval, each of which contained one emotionally neutral and one emotional (angry or happy) walker. Significant correlations with gait detection performance were observed for anger detection but not necessarily for happiness detection, implying that the detection of anger may be more strongly linked to explicit gait detection. This leads to a hypothesis that differential dependence may reflect the differential behavioural meaning between anger and happiness detection; it may be more crucial to localise or identify a person with anger than happiness.
Controlled but Independent: Effects of Mental Rotation and Developmental Dyslexia in Dual-Task Settings
Authors: Lachmann Thomas , Schumacher Bettina , van Leeuwen Cees
Published: June 2009

In two experiments, we compared the performance of normal-reading ( n = 26) and dyslexic children ( n = 22) in discriminating letters from their mirrored images. In experiment 1, they were always presented in the upright orientation; in experiment 2, they were presented in different angular orientations (0°, 90°, 180°). In order to determine whether task and dyslexia affect reaction times in early or late stages of processing, a dual-task paradigm was adopted in which the primary task was tone discrimination. Stimulus onset asynchrony (SOA) between first and second task was systematically varied (50 ms versus 400 ms). In both experiments dyslexics were slower overall than controls. No effects of mirror-image letters were found. In experiment 2, mental-rotation effects were additive with SOA. In accordance with earlier findings we concluded that the mental-rotation effect involves central processing capacity. Mental-rotation effects were the same for normal-reading and dyslexic children; mental rotation is not impaired in dyslexia. Remarkably, SOA effects were larger in normal readers than in dyslexics. This result was explained by observing that dyslexics experience decision difficulties already on the first task. As a result, they do not benefit optimally from increased latencies between first and second tasks.
Structural and kinetic modeling of an activating helix switch in the rhodopsin-transducin interface
Authors: Scheerer Patrick , Heck Martin , Goede Andrean , Park Jung Hee , Choe Hui-Woog , Ernst Oliver P. , Hofmann Klaus Peter , Hildebrand Peter W.
Published: June 2009

Extracellular signals prompt G protein-coupled receptors (GPCRs) to adopt an active conformation (R*) and catalyze GDP/GTP exchange in the α-subunit of intracellular G proteins (Gαβγ). Kinetic analysis of transducin (G
t
αβγ) activation shows that an intermediary R*·G
t
αβγ·GDP complex is formed that precedes GDP release and formation of the nucleotide-free R*·G protein complex. Based on this reaction sequence, we explore the dynamic interface between the proteins during formation of these complexes. We start from the R* conformation stabilized by a G
t
α C-terminal peptide (GαCT) obtained from crystal structures of the GPCR opsin. Molecular modeling allows reconstruction of the fully elongated C-terminal α-helix of G
t
α (α5) and shows how α5 can be docked to the open binding site of R*. Two modes of interaction are found. One of them – termed stable or S-interaction – matches the position of the GαCT peptide in the crystal structure and reproduces the hydrogen-bonding networks between the C-terminal reverse turn of GαCT and conserved E(D)RY and NPxxY(x)
5,6
F regions of the GPCR. The alternative fit – termed intermediary or I-interaction – is distinguished by a tilt (42°) and rotation (90°) of α5 relative to the S-interaction and shows different α5 contacts with the NPxxY(x)
5,6
F region and the second cytoplasmic loop of R*. From the 2 α5 interactions, we derive a “helix switch” mechanism for the transition of R*·G
t
αβγ·GDP to the nucleotide-free R*·G protein complex that illustrates how α5 might act as a transmission rod to propagate the conformational change from the receptor-G protein interface to the nucleotide binding site.
The double-stranded RNA-binding protein, PACT, is required for postnatal anterior pituitary proliferation
Authors: Peters Gregory A. , Seachrist Darcie D. , Keri Ruth A. , Sen Ganes C.
Published: June 2009

PACT is a double-stranded RNA-binding protein that also binds and activates the latent protein kinase, PKR, which plays a major role in cellular antiviral defense in mammals. For evaluating PACT's contribution to the innate immune system, Pact−/−mice have been generated; these mice exhibit notable developmental abnormalities including microtia, with craniofacial, ear, and hearing defects. Here we report that, in addition, Pact−/−mice had smaller body size and fertility defects, both of which were caused by defective pituitary functions. Pact−/−mice exhibited anterior pituitary lobe (AL) hypoplasia, which developed postnatally, when the second phase of pituitary expansion occurs. Among the 5 cell types in AL, the numbers of corticotrophs, gonadotrophs, and somatotrophs were equally decreased in Pact−/−mice with a greater impact on lactotrophs and a lesser impact on thyrotrophs. PACT mRNA and protein were highly expressed in the pituitary of wild-type (Wt) mice during the postnatal wave of AL proliferation, the same period in which the hypoplasia developed in Pact−/−mice. During this time, the pituitaries of Pact−/−mice did not exhibit significantly increased apoptosis compared with Wt mice but showed a decrease in cell proliferation. The inhibition of cell proliferation observed in vivo could be recapitulated in vitro in GH3 somato/lactotroph and LβT2 gonadotroph cell lines; knockdown of PACT expression with siRNA diminished the rate of proliferation of these cells. Our study revealed a physiologically significant role for PACT in cell proliferation and an essential role of a dsRNA-binding protein in mammalian pituitary expansion.
Nanogranular origin of concrete creep
Authors: Vandamme Matthieu , Ulm Franz-Josef
Published: June 2009

Concrete, the solid that forms at room temperature from mixing Portland cement with water, sand, and aggregates, suffers from time-dependent deformation under load. This creep occurs at a rate that deteriorates the durability and truncates the lifespan of concrete structures. However, despite decades of research, the origin of concrete creep remains unknown. Here, we measure the in situ creep behavior of calcium–silicate–hydrates (C–S–H), the nano-meter sized particles that form the fundamental building block of Portland cement concrete. We show that C–S–H exhibits a logarithmic creep that depends only on the packing of 3 structurally distinct but compositionally similar C–S–H forms: low density, high density, ultra-high density. We demonstrate that the creep rate (≈1/
t
) is likely due to the rearrangement of nanoscale particles around limit packing densities following the free-volume dynamics theory of granular physics. These findings could lead to a new basis for nanoengineering concrete materials and structures with minimal creep rates monitored by packing density distributions of nanoscale particles, and predicted by nanoscale creep measurements in some minute time, which are as exact as macroscopic creep tests carried out over years.
Adenosine A
2A
receptor is a unique angiogenic target of HIF-2α in pulmonary endothelial cells
Authors: Ahmad Aftab , Ahmad Shama , Glover Louise , Miller Stacy M. , Shannon John M. , Guo Xiaoling , Franklin Wilbur A. , Bridges James P. , Schaack Jerome B. , Colgan Sean P. , White Carl W.
Published: June 2009

Hypoxia, through the hypoxia-inducible transcription factors HIF-1α and HIF-2α (HIFs), induces angiogenesis by up-regulating a common set of angiogenic cytokines. Unlike HIF-1α, which regulates a unique set of genes, most genes regulated by HIF-2α overlap with those induced by HIF-1α. Thus, the unique contribution of HIF-2α remains largely obscure. By using adenoviral mutant HIF-1α and adenoviral mutant HIF-2α constructs, where the HIFs are transcriptionally active under normoxic conditions, we show that HIF-2α but not HIF-1α regulates adenosine A
2A
receptor in primary cultures of human lung endothelial cells. Further, siRNA knockdown of HIF-2α completely inhibits hypoxic induction of A
2A
receptor. Promoter studies show a 2.5-fold induction of luciferase activity with HIF-2α cotransfection. Analysis of the A
2A
receptor gene promoter revealed a hypoxia-responsive element in the region between −704 and −595 upstream of the transcription start site. By using a ChIP assay, we demonstrate that HIF-2α binding to this region is specific. In addition, we demonstrate that A
2A
receptor has angiogenic potential, as assessed by increases in cell proliferation, cell migration, and tube formation. Additional data show increased expression of A
2A
receptor in human lung tumor cancer samples relative to adjacent normal lung tissue. These data also demonstrate that A
2A
receptor is regulated by hypoxia and HIF-2α in human lung endothelial cells but not in mouse-derived endothelial cells.
Mesoscopic atomic entanglement for precision measurements beyond the standard quantum limit
Authors: Appel J. , Windpassinger P. J. , Oblak D. , Hoff U. B. , Kjærgaard N. , Polzik E. S.
Published: June 2009

Squeezing of quantum fluctuations by means of entanglement is a well-recognized goal in the field of quantum information science and precision measurements. In particular, squeezing the fluctuations via entanglement between 2-level atoms can improve the precision of sensing, clocks, metrology, and spectroscopy. Here, we demonstrate 3.4 dB of metrologically relevant squeezing and entanglement for ≳ 10
5
cold caesium atoms via a quantum nondemolition (QND) measurement on the atom clock levels. We show that there is an optimal degree of decoherence induced by the quantum measurement which maximizes the generated entanglement. A 2-color QND scheme used in this paper is shown to have a number of advantages for entanglement generation as compared with a single-color QND measurement.
Task-dependent organization of brain regions active during rest
Authors: Hasson Uri , Nusbaum Howard C. , Small Steven L.
Published: June 2009

The human brain demonstrates complex yet systematic patterns of neural activity at rest. We examined whether functional connectivity among those brain regions typically active during rest depends on ongoing and recent task demands and individual differences. We probed the temporal coordination among these regions during periods of language comprehension and during the rest periods that followed comprehension. Our findings show that the topography of this “rest network” varies with exogenous processing demands. The network encompassed more highly interconnected regions during rest than during listening, but also when listening to unsurprising vs. surprising information. Furthermore, connectivity patterns during rest varied as a function of recent listening experience. Individual variability in connectivity strength was associated with cognitive function: more attentive comprehenders demonstrated weaker connectivity during language comprehension, and a greater differentiation between connectivity during comprehension and rest. The regions we examined have generally been thought to form an invariant physiological and functional network whose activity reflects spontaneous cognitive processes. Our findings suggest that their function extends beyond the mediation of unconstrained thought, and that they play an important role in higher-level cognitive function.
Dendro-dendritic bundling and shared synapses between gonadotropin-releasing hormone neurons
Authors: Campbell Rebecca E. , Gaidamaka Galina , Han Seong-Kyu , Herbison Allan E.
Published: June 2009

The pulsatile release of gonadotropin-releasing hormone (GnRH) is critical for mammalian fertility, but the mechanisms underlying the synchronization of GnRH neurons are unknown. In the present study, the full extent of the GnRH neuron dendritic tree was visualized by patching and filling individual GnRH neurons with biocytin in acute brain slices from adult GnRH-green fluorescent protein (GFP) transgenic mice. Confocal analysis of 42 filled GnRH neurons from male and female adult mice revealed that the dendrites of the great majority of GnRH neurons (86%) formed multiple close appositions with dendrites of other GnRH neurons. Two types of interactions were encountered; the predominant interaction was one of vertical dendritic bundling where dendrites were found to wrap around each other in the same axis. The other interaction was one in which a GnRH neuron dendrite intercepted other GnRH neuron dendrites in a perpendicular fashion. Electron microscopy using pre-embedded, silver-enhanced immunogold labeling for both GnRH and GFP peptides in GnRH-GFP transgenic mice, confirmed that GnRH neuron dendrites were often immediately juxtaposed. Membrane specializations, including punctae and zonula adherens, were found connecting adjacent dendritic elements of GnRH neurons. Remarkably, individual afferent axon terminals were found to synapse with multiple GnRH neuron dendrites at sites of bundling. Together, these data demonstrate that GnRH neurons are not isolated from one another but, rather, interconnected via their long dendritic extensions. The observation of shared synaptic input to bundled GnRH neuron dendrites suggests a mechanism of GnRH neuron synchronization.
Lateral inferior prefrontal cortex and anterior cingulate cortex are engaged at different stages in the solution of insight problems
Authors: Anderson John R. , Anderson John F. , Ferris Jennifer L. , Fincham Jon M. , Jung Kwan-Jin
Published: June 2009

Two studies used puzzles that required participants to find a word that satisfied a set of constraints. The first study used a remote-association task, where participants had to find a word that would form compound words with 3 other words. The second study required participants to complete a word fragment with an associate of another word. Both studies produced distinct patterns of activity in the lateral inferior prefrontal cortex (LIPFC) and the anterior cingulate cortex (ACC). Activation in the LIPFC rose only as long as the participants were trying to retrieve the solution and dropped off as soon as the solution was obtained. However, activation in the ACC increased upon the retrieval of a solution, reflecting the need to process that solution. The data of the second experiment are fit by an information-processing model that interprets the activity in the LIPFC as reflecting retrieval operations and the activity in the ACC as reflecting subgoal setting.
Computing protein stabilities from their chain lengths
Authors: Ghosh Kingshuk , Dill Ken A.
Published: June 2009

New amino acid sequences of proteins are being learned at a rapid rate, thanks to modern genomics. The native structures and functions of those proteins can often be inferred using bioinformatics methods. We show here that it is also possible to infer the stabilities and thermal folding properties of proteins, given only simple genomics information: the chain length and the numbers of charged side chains. In particular, our model predicts Δ
H
(
T
), Δ
S
(
T
), Δ
C

p

, and Δ
F
(
T
) —the folding enthalpy, entropy, heat capacity, and free energy—as functions of temperature
T
; the denaturant
m
values in guanidine and urea; the pH-temperature-salt phase diagrams, and the energy of confinement
F
(
s
) of the protein inside a cavity of radius
s
. All combinations of these phase equilibria can also then be computed from that information. As one illustration, we compute the pH and salt conditions that would denature a protein inside a small confined cavity. Because the model is analytical, it is computationally efficient enough that it could be used to automatically annotate whole proteomes with protein stability information.
Modulation of intein activity by its neighboring extein substrates
Authors: Amitai Gil , Callahan Brian P. , Stanger Matt J. , Belfort Georges , Belfort Marlene
Published: June 2009

Inteins comprise a large family of phylogenetically widespread self-splicing protein catalysts that colonize diverse host proteins. The evolutionary and functional relationship between the intein and the split-host protein, the exteins, is largely unknown. To probe an association, we developed an in vivo and in vitro intein assay based on FRET. The FRET assay reports cleavage of the intein from its N-terminal extein. Applying this assay to randomized extein libraries, we show that the nature of the extein substrate bordering the intein can profoundly influence intein activity. Residues proximal to the intein-splicing junction in both N- and C-terminal exteins can accelerate the N-terminal cleavage rate by >4-fold or attenuate cleavage by 1,000-fold, both resulting in compromised self-splicing efficiency. The existence and the magnitude of extein effects require consideration for maximizing the utility of inteins in biotechnological applications, and they predict biases in intein integration sites in nature.
Signaling mechanisms involved in altered function of macrophages from diet-induced obese mice affect immune responses
Authors: Zhou Qingde , Leeman Susan E. , Amar Salomon
Published: June 2009

Recent research links diet-induced obesity (DIO) with impaired immunity, although the underlying mechanisms remain unclear. We find that the induction of inducible NO synthase (iNOS) and cytokines is suppressed in mice with DIO and in bone marrow macrophages (BMMΦ) from mice with DIO exposed to an oral pathogen,Porphyromonas gingivalis. BMMΦ from lean mice pre-treated with free fatty acids (FFAs) and exposed toP. gingivalisalso exhibit a diminished induction of iNOS and cytokines. BMMΦ from lean and obese mice exposed toP. gingivalisand analyzed by a phosphorylation protein array show a reduction of Akt only in BMMΦ from mice with DIO. This reduction is responsible for diminished NF-κB activation and diminished induction of iNOS and cytokines. We next observed that Toll-like receptor 2 (TLR2) is suppressed in BMMΦ from DIO mice whereas carboxy-terminal modulator protein (CTMP), a known suppressor of Akt phosphorylation, is elevated. This elevation stems from defective TLR2 signaling. In BMMΦ from lean mice, both FFAs and TNF-α—via separate pathways—induce an increase in CMTP. However, in BMMΦ from DIO mice, TLR2 can no longer inhibit the TNF-α-induced increase in CTMP caused byP. gingivalischallenge. This defect can then be restored by transfecting WT TLR2 into BMMΦ from DIO mice. Thus, feeding mice a high-fat diet over time elevates the CTMP intracellular pool, initially via FFAs activating TLR2 and later when the defective TLR2 is unable to inhibit TNF-α-induced CTMP. These findings unveil a link between obesity and innate immunity.
ClpXP protease degrades the cytoskeletal protein, FtsZ, and modulates FtsZ polymer dynamics
Authors: Camberg Jodi L. , Hoskins Joel R. , Wickner Sue
Published: June 2009

FtsZ is the major cytoskeletal protein in bacteria and a tubulin homologue. It polymerizes and forms a ring where constriction occurs to divide the cell. We found that FtsZ is degraded by
E. coli
ClpXP, an ATP-dependent protease. In vitro, ClpXP degrades both FtsZ protomers and polymers; however, polymerized FtsZ is degraded more rapidly than the monomer. Deletion analysis shows that the N-terminal domain of ClpX is important for polymer recognition and that the FtsZ C terminus contains a ClpX recognition signal. In vivo, FtsZ is turned over slower in a
clpX
deletion mutant compared with a WT strain. Overexpression of ClpXP results in increased FtsZ degradation and filamentation of cells. These results suggest that ClpXP may participate in cell division by modulating the equilibrium between free and polymeric FtsZ via degradation of FtsZ filaments and protomers.
MEMS-based microspectrometer technologies for NIR and MIR wavelengths
Authors: Schuler Leo P , Milne Jason S , Dell John M , Faraone Lorenzo
Published: June 2009

Commercially manufactured near-infrared (NIR) instruments became available about 50 years ago. While they have been designed for laboratory use in a controlled environment and boast high performance, they are generally bulky, fragile and maintenance intensive, and therefore expensive to purchase and maintain.

Micromachining is a powerful technique to fabricate micromechanical parts such as integrated circuits. It was perfected in the 1980s and led to the invention of micro electro mechanical systems (MEMSs). The three characteristic features of MEMS fabrication technologies are miniaturization, multiplicity and microelectronics. Combined, these features allow the batch production of compact and rugged devices with integrated intelligence. In order to build more compact, more rugged and less expensive NIR instruments, MEMS technology has been successfully integrated into a range of new devices.

In the first part of this paper we discuss the UWA MEMS-based Fabry–Pérot spectrometer, its design and issues to be solved. MEMS-based Fabry–Pérot filters primarily isolate certain wavelengths by sweeping across an incident spectrum and the resulting monochromatic signal is detected by a broadband detector. In the second part, we discuss other microspectrometers including other Fabry–Pérot spectrometer designs, time multiplexing devices and mixed time/space multiplexing devices.
Tricellulin Forms a Barrier to Macromolecules in Tricellular Tight Junctions without Affecting Ion Permeability
Authors: Krug Susanne M. , Amasheh Salah , Richter Jan F. , Milatz Susanne , Günzel Dorothee , Westphal Julie K. , Huber Otmar , Schulzke Jörg D. , Fromm Michael
Published: June 2009

Tricellulin is a tight junction protein localized in tricellular tight junctions (tTJs), the meeting points of three cells, but also in bicellular tight junctions (bTJs). To investigate its specific barrier functions in bTJs and tTJs, TRIC-a was expressed in low-level tricellulin–expressing cells, and MDCK II, either in all TJs or only in tTJs. When expressed in all TJs, tricellulin increased paracellular electrical resistance and decreased permeability to ions and larger solutes, which are associated with enhanced ultrastructural integrity of bTJs toward enhanced strand linearity. In tTJs in contrast, ultrastructure was unchanged and tricellulin minimized permeability to macromolecules but not to ions. This paradox is explained by properties of the tTJ central tube which is wide enough for passage of macromolecules, but too rare to contribute significantly to ion permeability. In conclusion, at low tricellulin expression the tTJ central tube forms a pathway for macromolecules. At higher expression, tricellulin forms a barrier in tTJs effective only for macromolecules and in bTJs for solutes of all sizes.
An investigation into the population abundance distribution of mRNAs, proteins, and metabolites in biological systems
Authors: Lu Chuan , King Ross D.
Published: June 2009

Motivation: Distribution analysis is one of the most basic forms of statistical analysis. Thanks to improved analytical methods, accurate and extensive quantitative measurements can now be made of the mRNA, protein and metabolite from biological systems. Here, we report a large-scale analysis of the population abundance distributions of the transcriptomes, proteomes and metabolomes from varied biological systems.

Results: We compared the observed empirical distributions with a number of distributions: power law, lognormal, loglogistic, loggamma, right Pareto-lognormal (PLN) and double PLN (dPLN). The best-fit for mRNA, protein and metabolite population abundance distributions was found to be the dPLN. This distribution behaves like a lognormal distribution around the centre, and like a power law distribution in the tails. To better understand the cause of this observed distribution, we explored a simple stochastic model based on geometric Brownian motion. The distribution indicates that multiplicative effects are causally dominant in biological systems. We speculate that these effects arise from chemical reactions: the central-limit theorem then explains the central lognormal, and a number of possible mechanisms could explain the long tails: positive feedback, network topology, etc. Many of the components in the central lognormal parts of the empirical distributions are unidentified and/or have unknown function. This indicates that much more biology awaits discovery.

Contact:  rdk@aber.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Modeling multi-cellular behavior in epidermal tissue homeostasis via finite state machines in multi-agent systems
Authors: Sütterlin Thomas , Huber Simone , Dickhaus Hartmut , Grabe Niels
Published: June 2009

Motivation: For the efficient application of multi-agent systems to spatial and functional modeling of tissues flexible and intuitive modeling tools are needed, which allow the graphical specification of cellular behavior in a tissue context without presuming specialized programming skills.

Results: We developed a graphical modeling system for multi-agent based simulation of tissue homeostasis. An editor allows the intuitive and hierarchically structured specification of cellular behavior. The models are then automatically compiled into highly efficient source code and dynamically linked to an interactive graphical simulation environment. The system allows the quantitative analysis of the morphological and functional tissue properties emerging from the cell behavioral model. We demonstrate the relevance of the approach using a recently published model of epidermal homeostasis as well as a series of cell-cycle models.

Availability: The complete software is available in binary executables for MS-Windows and Linux at tiga.uni-hd.de

Contact:  niels.grabe@bioquant.uni-heidelberg.de
A statistical framework for protein quantitation in bottom-up MS-based proteomics
Authors: Karpievitch Yuliya , Stanley Jeff , Taverner Thomas , Huang Jianhua , Adkins Joshua N. , Ansong Charles , Heffron Fred , Metz Thomas O. , Qian Wei-Jun , Yoon Hyunjin , Smith Richard D. , Dabney Alan R.
Published: June 2009

Motivation: Quantitative mass spectrometry-based proteomics requires protein-level estimates and associated confidence measures. Challenges include the presence of low quality or incorrectly identified peptides and informative missingness. Furthermore, models are required for rolling peptide-level information up to the protein level.

Results: We present a statistical model that carefully accounts for informative missingness in peak intensities and allows unbiased, model-based, protein-level estimation and inference. The model is applicable to both label-based and label-free quantitation experiments. We also provide automated, model-based, algorithms for filtering of proteins and peptides as well as imputation of missing values. Two LC/MS datasets are used to illustrate the methods. In simulation studies, our methods are shown to achieve substantially more discoveries than standard alternatives.

Availability: The software has been made available in the open-source proteomics platform DAnTE (http://omics.pnl.gov/software/).

Contact:  adabney@stat.tamu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Automated protein (re)sequencing with MS/MS and a homologous database yields almost full coverage and accuracy
Authors: Liu Xiaowen , Han Yonghua , Yuen Denis , Ma Bin
Published: June 2009

Motivation: The bottom-up tandem mass spectrometry (MS/MS) is regularly used in proteomics nowadays for identifying proteins from a sequence database. De novo sequencing software is also available for sequencing novel peptides with relatively short sequence lengths. However, automated sequencing of novel proteins from MS/MS remains a challenging problem.

Results: Very often, although the target protein is novel, it has a homologous protein included in a known database. When this happens, we propose a novel algorithm and automated software tool, named Champs, for sequencing the complete protein from MS/MS data of a few enzymatic digestions of the purified protein. Validation with two standard proteins showed that our automated method yields >99% sequence coverage and 100% sequence accuracy on these two proteins. Our method is useful to sequence novel proteins or ‘re-sequence’ a protein that has mutations comparing with the database protein sequence.

Availability: The software, named Champs (Complete Homology-Assisted Ms/ms Protein Sequencing), and the MS/MS data used in the article, are freely available at http://monod.uwaterloo.ca/champs/.

Contact:  binma@uwaterloo.ca

Supplementary information:  Supplementary data are available at Bioinformatics online.
Reliable prediction of protein thermostability change upon double mutation from amino acid sequence
Authors: Huang Liang-Tsung , Gromiha M. Michael
Published: June 2009

Summary: The accurate prediction of protein stability change upon mutation is one of the important issues for protein design. In this work, we have focused on the stability change of double mutations and systematically analyzed the wild-type and mutant residues, patterns in amino acid sequence and locations of mutants. Based on the sequence information of wild-type, mutant and three neighboring residues, we have presented a weighted decision table method (WET) for predicting the stability changes of 180 double mutants obtained from thermal (ΔΔG) denaturation. Using 10-fold cross-validation test, our method showed a correlation of 0.75 between experimental and predicted values of stability changes, and an accuracy of 82.2% for discriminating the stabilizing and destabilizing mutants.

Availability:  http://bioinformatics.myweb.hinet.net/wetstab.htm

Contact:  michael-gromiha@aist.go.jp

Supplementary information:  Supplementary data are available at Bioinformatics online.
A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6
Authors: Bengtsson Henrik , Wirapati Pratyaksha , Speed Terence P.
Published: June 2009

Motivation: High-resolution copy-number (CN) analysis has in recent years gained much attention, not only for the purpose of identifying CN aberrations associated with a certain phenotype, but also for identifying CN polymorphisms. In order for such studies to be successful and cost effective, the statistical methods have to be optimized. We propose a single-array preprocessing method for estimating full-resolution total CNs. It is applicable to all Affymetrix genotyping arrays, including the recent ones that also contain non-polymorphic probes. A reference signal is only needed at the last step when calculating relative CNs.

Results: As with our method for earlier generations of arrays, this one controls for allelic crosstalk, probe affinities and PCR fragment-length effects. Additionally, it also corrects for probe sequence effects and co-hybridization of fragments digested by multiple enzymes that takes place on the latest chips. We compare our method with Affymetrix's CN5 method and the dChip method by assessing how well they differentiate between various CN states at the full resolution and various amounts of smoothing. Although CRMA v2 is a single-array method, we observe that it performs as well as or better than alternative methods that use data from all arrays for their preprocessing. This shows that it is possible to do online analysis in large-scale projects where additional arrays are introduced over time.

Availability: A bounded-memory implementation that can process any number of arrays is available in the open source R package aroma.affymetrix.

Contact:  hb@stat.berkeley.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
A fast hybrid short read fragment assembly algorithm
Authors: Schmidt Bertil , Sinha Ranjan , Beresford-Smith Bryan , Puglisi Simon J.
Published: June 2009

Summary: The shorter and vastly more numerous reads produced by second-generation sequencing technologies require new tools that can assemble massive numbers of reads in reasonable time. Existing short-read assembly tools can be classified into two categories: greedy extension-based and graph-based. While the graph-based approaches are generally superior in terms of assembly quality, the computer resources required for building and storing a huge graph are very high. In this article, we present Taipan, an assembly algorithm which can be viewed as a hybrid of these two approaches. Taipan uses greedy extensions for contig construction but at each step realizes enough of the corresponding read graph to make better decisions as to how assembly should continue. We show that this approach can achieve an assembly quality at least as good as the graph-based approaches used in the popular Edena and Velvet assembly tools using a moderate amount of computing resources.

Availability and Implementation: Source code in C running on Linux is freely available at http://taipan.sourceforge.net

Contact:  asbschmidt@ntu.edu.sg
A New Flow Cytometry Technique to IdentifyPhaeomoniella chlamydosporaExopolysaccharides and Study Mechanisms of Esca Grapevine Foliar Symptoms
Authors: Andolfi A. , Cimmino A. , Evidente A. , Iannaccone M. , Capparelli R. , Mugnai L. , Surico G.
Published: June 2009

A flow cytometry technique that unequivocally identifies some of the toxic metabolites produced by Phaeomoniella chlamydospora, one of the main fungal pathogens causing esca disease of grapevine (Vitis vinifera), was developed. Antibodies raised against exopolysaccharides (EPS)—metabolites produced by Pa. chlamydospora that have been reported to be phytotoxic—were used as antigen to immunize rats. The specificity of these antibodies was assayed by flow cytometry against Pa. chlamydospora polysaccharides and against EPS with a different structure isolated from other phytopathogenic fungi, including Phaeoacremonium aleophilum and the Botryosphaeriaceae species Neofusicoccum luteum and N. parvum. Using this method, Pa. chlamydospora polysaccharides were detected in the symptomatic leaves of esca-affected grapevines, while healthy and asymptomatic leaves from both healthy and diseased vines did not produce a binding reaction. This method potentially could be used to develop a simple kit to study the mechanisms underlying the development of esca foliar symptoms and to indirectly assess the presence of Pa. chlamydospora in grapevine material.
A New Expanded Host Range of Cucurbit yellow stunting disorder virus Includes Three Agricultural Crops
Authors: Wintermantel William M. , Hladky Laura L. , Cortez Arturo A. , Natwick Eric T.
Published: June 2009

Cucurbit yellow stunting disorder virus (CYSDV) was identified in the fall of 2006 affecting cucurbit production in the southwestern United States (California, Arizona), as well as in nearby Sonora, Mexico, resulting in nearly universal infection of fall melon crops in 2006 and 2007, and late infection of 2007 spring melons. Survival of CYSDV through the largely cucurbit-free winter months suggested the presence of weed or alternate crop hosts, although previous studies indicated a limited host range restricted to members of the Cucurbitaceae. To determine potential reservoir hosts for CYSDV in desert production, weed and crop hosts were collected from throughout the region over a period of 26 months, and were tested for the presence of CYSDV by reverse transcription–polymerase chain reaction (RT-PCR) using CYSDV HSP70h- and coat protein gene–specific primers. Many noncucurbits collected from infected melon fields and nearby areas were symptomless and virus free; however, CYSDV was detected in alfalfa (Medicago sativa), lettuce (Lactuca sativa), and snap bean (Phaseolus vulgaris), as well as in several weed species widely prevalent in the region. Typical crinivirus symptoms of interveinal yellowing and leaf brittleness were observed on CYSDV-infected snap bean, alkali mallow (Sida hederacea) and Wright's groundcherry (Physalis wrightii), while other infected crop and weed hosts were symptomless. Transmission tests demonstrated that lettuce, snap bean, alkali mallow, Wright's groundcherry, and buffalo gourd (Cucurbita foetidissima) could serve as virus reservoir hosts for transmission of CYSDV to melon and other cucurbits. These results expand the previously known host range of CYSDV, demonstrating that the virus is capable of infecting not only members of the Cucurbitaceae, but also plants in seven additional taxonomic families.
A Soilless Verticillium Wilt Assay Using an Early Flowering Lettuce Line
Authors: Klosterman Steven J. , Hayes Ryan J.
Published: June 2009

A soilless growth chamber assay was evaluated for rapid assessment of Verticillium wilt on lettuce (Lactuca sativa). Seedlings of the early flowering Plant Introduction (PI) 251246 were inoculated in tubes with conidial suspensions of isolates of Verticillium dahliae from lettuce or cauliflower. PI 251246 developed significant leaf and root symptoms by 21 days following inoculation with isolates of race 1 and race 2 from lettuce, but not following inoculation with an isolate from cauliflower. In contrast, leaf symptoms on the cultivar La Brillante and root symptoms on the cultivar Salinas were not easily differentiated from the symptoms observed on the noninoculated control treatments in the soilless assay, even at the highest inoculum concentration of 1 × 107conidia/ml. Comparison of the soilless growth chamber assay and a soil-based greenhouse assay revealed a significantly higher proportion of PI 251246 with root vascular discoloration in the soilless assay compared with the soil-based greenhouse assay (χ2, 1 df = 8.9; P = 0.003). There is thus an advantage to using the soilless growth chamber assay with PI 251246. Compared with the soil-based greenhouse assay, the soilless assay reduced the time required for evaluation of Verticillium wilt symptoms on lettuce from about 90 days to 42 days.