bluuebunny/crossref_metadata_2025 huggingface dataset:
Class A scavenger receptors regulate tolerance against apoptotic cells, and autoantibodies against these receptors are predictive of systemic lupus
Authors: Wermeling Fredrik , Chen Yunying , Pikkarainen Timo , Scheynius Annika , Winqvist Ola , Izui Shozo , Ravetch Jeffrey V. , Tryggvason Karl , Karlsson Mikael C.I.
Published: September 2007

Apoptotic cells are considered to be a major source for autoantigens in autoimmune diseases such as systemic lupus erythematosus (SLE). In agreement with this, defective clearance of apoptotic cells has been shown to increase disease susceptibility. Still, little is known about how apoptotic cell–derived self-antigens activate autoreactive B cells and where this takes place. In this study, we find that apoptotic cells are taken up by specific scavenger receptors expressed on macrophages in the splenic marginal zone and that mice deficient in these receptors have a lower threshold for autoantibody responses. Furthermore, antibodies against scavenger receptors are found before the onset of clinical symptoms in SLE-prone mice, and they are also found in diagnosed SLE patients. Our findings describe a novel mechanism where autoantibodies toward scavenger receptors can alter the response to apoptotic cells, affect tolerance, and thus promote disease progression. Because the autoantibodies can be detected before onset of disease in mice, they could have predictive value as early indicators of SLE.
Selective predisposition to bacterial infections in IRAK-4–deficient children: IRAK-4–dependent TLRs are otherwise redundant in protective immunity
Authors: Ku Cheng-Lung , von Bernuth Horst , Picard Capucine , Zhang Shen-Ying , Chang Huey-Hsuan , Yang Kun , Chrabieh Maya , Issekutz Andrew C. , Cunningham Coleen K. , Gallin John , Holland Steven M. , Roifman Chaim , Ehl Stephan , Smart Joanne , Tang Mimi , Barrat Franck J. , Levy Ofer , McDonald Douglas , Day-Good Noorbibi K. , Miller Richard , Takada Hidetoshi , Hara Toshiro , Al-Hajjar Sami , Al-Ghonaium Abdulaziz , Speert David , Sanlaville Damien , Li Xiaoxia , Geissmann Frédéric , Vivier Eric , Maródi László , Garty Ben-Zion , Chapel Helen , Rodriguez-Gallego Carlos , Bossuyt Xavier , Abel Laurent , Puel Anne , Casanova Jean-Laurent
Published: September 2007

Human interleukin (IL) 1 receptor–associated kinase 4 (IRAK-4) deficiency is a recently discovered primary immunodeficiency that impairs Toll/IL-1R immunity, except for the Toll-like receptor (TLR) 3– and TLR4–interferon (IFN)-a/b pathways. The clinical and immunological phenotype remains largely unknown. We diagnosed up to 28 patients with IRAK-4 deficiency, tested blood TLR responses for individual leukocyte subsets, and TLR responses for multiple cytokines. The patients' peripheral blood mononuclear cells (PBMCs) did not induce the 11 non-IFN cytokines tested upon activation with TLR agonists other than the nonspecific TLR3 agonist poly(I:C). The patients' individual cell subsets from both myeloid (granulocytes, monocytes, monocyte-derived dendritic cells [MDDCs], myeloid DCs [MDCs], and plasmacytoid DCs) and lymphoid (B, T, and NK cells) lineages did not respond to the TLR agonists that stimulated control cells, with the exception of residual responses to poly(I:C) and lipopolysaccharide in MDCs and MDDCs. Most patients (22 out of 28; 79%) suffered from invasive pneumococcal disease, which was often recurrent (13 out of 22; 59%). Other infections were rare, with the exception of severe staphylococcal disease (9 out of 28; 32%). Almost half of the patients died (12 out of 28; 43%). No death and no invasive infection occurred in patients older than 8 and 14 yr, respectively. The IRAK-4–dependent TLRs and IL-1Rs are therefore vital for childhood immunity to pyogenic bacteria, particularly Streptococcus pneumoniae. Conversely, IRAK-4–dependent human TLRs appear to play a redundant role in protective immunity to most infections, at most limited to childhood immunity to some pyogenic bacteria.
Staphylococcal complement evasion by various convertase-blocking molecules
Authors: Jongerius Ilse , Köhl Jörg , Pandey Manoj K. , Ruyken Maartje , van Kessel Kok P.M. , van Strijp Jos A.G. , Rooijakkers Suzan H.M.
Published: September 2007

To combat the human immune response, bacteria should be able to divert the effectiveness of the complement system. We identify four potent complement inhibitors in Staphylococcus aureus that are part of a new immune evasion cluster. Two are homologues of the C3 convertase modulator staphylococcal complement inhibitor (SCIN) and function in a similar way as SCIN. Extracellular fibrinogen-binding protein (Efb) and its homologue extracellular complement-binding protein (Ecb) are identified as potent complement evasion molecules, and their inhibitory mechanism was pinpointed to blocking C3b-containing convertases: the alternative pathway C3 convertase C3bBb and the C5 convertases C4b2aC3b and C3b2Bb. The potency of Efb and Ecb to block C5 convertase activity was demonstrated by their ability to block C5a generation and C5a-mediated neutrophil activation in vitro. Further, Ecb blocks C5a-dependent neutrophil recruitment into the peritoneal cavity in a mouse model of immune complex peritonitis. The strong antiinflammatory properties of these novel S. aureus–derived convertase inhibitors make these compounds interesting drug candidates for complement-mediated diseases.
Structural basis for complement factor H–linked age-related macular degeneration
Authors: Prosser Beverly E. , Johnson Steven , Roversi Pietro , Herbert Andrew P. , Blaum Bärbel S. , Tyrrell Jess , Jowitt Thomas A. , Clark Simon J. , Tarelli Edward , Uhrín Dušan , Barlow Paul N. , Sim Robert B. , Day Anthony J. , Lea Susan M.
Published: September 2007

Nearly 50 million people worldwide suffer from age-related macular degeneration (AMD), which causes severe loss of central vision. A single-nucleotide polymorphism in the gene for the complement regulator factor H (FH), which causes a Tyr-to-His substitution at position 402, is linked to ∼50% of attributable risks for AMD. We present the crystal structure of the region of FH containing the polymorphic amino acid His402 in complex with an analogue of the glycosaminoglycans (GAGs) that localize the complement regulator on the cell surface. The structure demonstrates direct coordination of ligand by the disease-associated polymorphic residue, providing a molecular explanation of the genetic observation. This glycan-binding site occupies the center of an extended interaction groove on the regulator's surface, implying multivalent binding of sulfated GAGs. This finding is confirmed by structure-based site-directed mutagenesis, nuclear magnetic resonance–monitored binding experiments performed for both H402 and Y402 variants with this and another model GAG, and analysis of an extended GAG–FH complex.
Relabeling of the K2 Rydberg States
Authors: Xie Feng , Li Dan , Li Li
Published: September 2007

The K2 electronic states calculated theoretically and/or observed experimentally have been relabeled according to their dominant hydrogenic nl characters of the Rydberg orbitals. These states can be divided into core-penetrating and core-nonpenetrating states. This classification provides physical insights for interpreting and predicting experimental observations. The application of this method to K2 is compared with that to Na2 and Li2.
UV Photodissociation Dynamics of HN3 in 190-248 nm
Authors: Zhang Jian-yang , Yuan Kai-jun , Cheng Yuan , Harich Steven A. , Wang Xiu-yan , Yang Xue-ming , Wodtke Alec M.
Published: September 2007

The H+N3 channel in the ultraviolet photodissociation of HN3 has been investigated from 190 nm to {248 nm} using the high-n Rydberg H-atom time-of-flight technique. Product translational energy distributions as well as product angular anisotropy parameters were determined for the H+N3 channel at different photolysis wavelengths. N3 vibrational state distribution has also been derived from the product translational energy distribution at these wavelengths. Above photolysis wavelength 225 nm, HN3 predominantly dissociate through the repulsive state. Below 225 nm, a new slow channel starts to appear at 220 nm in addition to the existing channel. This channel is attributed to a ring closure dissociation channel to produce the cyclic N3 product. As photolysis energy increases, this new channel becomes more important.
Observation of a New 2 Excited Electronic State of SF by Resonance-Enhanced Multiphoton Ionization Spectroscopy
Authors: Zheng Xian-feng , Wang Ting-ting , Li Chun-yan , Chen Yang , Zhang Jing-song
Published: September 2007

The (2+1) resonance-enhanced multiphoton ionization (REMPI) spectrum of SF has been obtained in the single-photon wavelength region of 307-321 nm. Five vibronic bands were observed and assigned to the two-photon transitions from the ground state to a 2 Rydberg state. The term value Te, vibrational frequency, and the rotational constant of the 2 Rydberg state were determined. Another 2P state was observed near 312 nm.
Near-UV Photodissociation Dynamics of Thiomethoxy Radical viaA2A1 State: H-atom Product Channel
Authors: Zheng Xian-feng , Song Yu , Wu Jing-ze , Zhang Jing-song
Published: September 2007

Photodissociation dynamics of jet-cooled thiomethoxy radical (CH3S) via the A2A1 X2E transition is investigated near 352 nm. The H-atom product channel is observed directly for the first time by H-atom product yield spectrum and photofragment translational spectroscopy. The 2132 vibrational level of the A2A1 state dissociates to the H+H2CS products. The H+H2CS product translational energy release is modest and peaks around 33 kJ/mol; the H-atom angular distribution is isotropic. The dissociation mechanism is consistent with internal conversion of the excited A2A1 state to the X2E ground state and subsequent unimolecular dissociation on the ground state to the H+H2CS products.
Reaction of CH2Cl with O2
Authors: Ma Hai-tao , Shi Cong-yun , Bian Wen-sheng , Su Hong-mei , Kong Fan-ao
Published: September 2007

The elementary reaction of CH2Cl+O2 in gas phase was investigated by time-resolved FTIR emission spectroscopy. Vibrationally excited products CO (v 4), and CO2 (3, v 7) were observed. The yield ratio of CO/CO2(3) was 72.27. The reaction pathways were studied theoretically at QCISD//UB3LYP/6-311++G(d,p) level. In the beginning of the reaction, CH2Cl radical associated with O2 to form CH2ClOO, followed by removal of the Cl atom to yield another intermediate dioxirane CH2OO. Subsequently, a series of isomerization and decomposition of the CH2OO took place, yielding the final products of CO and CO2. The calculated result was in consistent with the experimental observation.
Photofragment Imaging of HNCO Decomposition at 210 nm: the Primary NH(a1)+CO(X1+) Channel
Authors: Wang Hua , Liu Shi-lin , Liu Jie , Wang Feng-yan , Jiang Bo , Yang Xue-ming
Published: September 2007

The photodissociation of isocyanic acid (HNCO) on the first excited singlet state following the excitation at 210 nm was investigated with an ion velocity slice imaging technique by probing the CO fragment. It was found from the (2+1) resonance-enhanced multi-photon ionization (REMPI) spectrum that the CO fragments are rotationally hot with population up to Jmax=50. The velocity imagings of the CO fragments at JCO=30 and 35 indicate that formation of NH(a1)+CO(X1+, v=0) is the predominant dissociation channel at 210 nm. From analysis of the CO fragment translational energy distributions, the NH(a1) fragment was observed to be rotationally cold, about half of the available energy was partitioned into the translational motion of fragments after dissociation, and the NH(a1)+CO(X1+) dissociation threshold was determined at 4273830 cm1. From analysis of the CO fragment angular distributions, the dissociation anisotropy parameter was found to be negative, and increasing with the rotational quantum number of the NH fragment, i.e., from -0.75 at JNH=2-4 to -0.17 at JNH=11. Impulsive direct and vertical dissociation process of HNCO on the singlet state at 210 nm was confirmed experimentally. A classical impact dissociation model was employed to explain the dependence of the value on the rotational excitation of the NH fragment.
Photoinduced Electron and H-atom Transfer Reactions of Xanthone by Laser Flash Photolysis
Authors: Wang Jin-ting , Pan Yang , Zhang Li-min , Yu Shu-qin
Published: September 2007

The property of the lowest excited triplet states of xanthone in acetonitrile was investigated using time-resolved laser flash photolysis at 355 nm. The transient absorption spectra and the quenching rate constants (kq) of the excited xanthone with several amines were determined. Good correlation between lgkq and the driving force of the reactions suggests the electron transfer mechanism, except aniline and 3-nitroaniline (3-NO2-A) which showed energy transfer mechanism. With the appearance of ketyl radical, hydrogen atom transfer also happened between xanthone and dimethyl-p-toluidine, 3,5,N,N-tetramethylaniline, N,N-dimethylaniline, and triethylamine. Therefore, both electron transfer and H-atom transfer occured in these systems. Great discrepancies of kq values were discovered in H-atom abstraction reactions for alcohols and phenols, which can be explained by different abstraction mechanisms. The quenching rate constants between xanthone and alcohols correlate well with the -C-H bonding energy of alcohols.
Photodissociation Dynamics of Nitromethane and Nitroethane at 266 nm
Authors: Yue Xian-fang , Sun Ju-long , Wei Qiang , Yin Hong-ming , Han Ke-li
Published: September 2007

Measurements of the nascent OH product from photodissociation of gaseous nitromethane and nitroethane at 266 nm were performed using the single-photon laser induced fluorescence technique. The OH fragment is found to be vibrationally cold for both systems. The rotational state distribution of nitromethane are Boltzmann, with rotational temperature of Trot=2045150 and 1923150 K for both 23/2 and 21/2 states, respectively. For nitroethane, the rotational state distribution shows none Boltzmann and cannot be well characterized by a rotational temperature, which indicates the different mechanisms in producing OH radicals from photodissociation of nitromethane and nitroethane. The rotational energy is calculated as 14.360.8 and 4.980.8 kJ/mol for nitromethane and nitroethane, respectively. A preferential population of the low spin-orbit component (23/2) is observed for both nitromethane and nitroethane. The dominant population of + state in two -doublet states is also observed for both nitromethane and nitroethane, which indicates that the unpaired lobe of the OH fragment is parallel to the plane of rotation.
Predissociation Dynamics of B State of Methyl Iodide with Femtosecond Pump-probe Technique
Authors: Wei Zheng-rong , Zhang Feng , Wang Yan-mei , Zhang Bing
Published: September 2007

The predissociation dynamics of B Rydberg state of methyl iodide has been studied with femtosecond two-color pump-probe time-of-flight spectra at pump pulse of 400nm and probe pulse 800 nm. The dominant product channels are the CH3I+ and CH3+ formation. The time-dependent signals for CH3I+ and CH3+ ions are obtained. Both of the signal curves can be fitted by biexponential decays with time constants of O 1 and O 2, O 1 was assigned to the lifetimes of high Rydberg states, which can be accessed by absorbing three 400 nm pump pulses and O 2 reflects the dynamics of B Rydberg state, which is accessed with two pump pulses. The lifetime of B Rydberg state is determined to be about 1.57 ps, which is incredibly consistent with the previous studies. The results were interpreted as a multiphoton dissociative ionization processes.
Electron Transfer Theory Revisit: Motional Narrowing Induced Non-Markovian Rate Processes
Authors: Chen Ying , Xua Rui-xue , Ke Hong-wei , Yan Yi-jing
Published: September 2007

While the exact theory of chemical reaction rate processes is always non-Markovian, experimental rates do often show practically Markovian that supports kinetics rate constant description. In this work, we propose to use the Kubo's motional narrowing line shape function to characterize the Markovian character of the simplest two-state electron transfer reaction system. On the basis of analytical results, we demonstrate the related Markovianicity parameter as an interplay between the fluctuating solvent environment and the coherent transfer coupling. It is found that a non-Markovian rate process is most likely to occur in a symmetric system in the fast solvent modulation regime, where the resonant tunneling enhancement plays the important role. The effect of quantum solvation on electron transfer, which is dominant in the fast modulation regime, will also be highlighted.
Mode of Myosin Transportation in Living Cells Studied by Single Particle Tracking
Authors: Liang Zhang-yi , Xu Ning , Guan Ying-hua , Zhang You-yi , Zhao Xin-sheng
Published: September 2007

The transport of internalized 1A-adrenergic receptor (1A-AR) by myosin protein in live cells was studied. The technique of single particle tracking by fluorescence imaging with high temporal and spatial resolution was used. The endosomes of 1A-AR were transported along actin filaments in a step-by-step mode. The average step-size in different time resolutions is consistent with the step-size of myosin assay in vitro. With the simulation of the stepwise traces in different time resolutions, we found that the kinetic process of each step is in coherence with the single myosin assay in vitro.
Intermolecular Hydrogen Bonds Formed Between Amino Acid Molecules in Aqueous Solution Investigated by Temperature-jump Nanosecond Time-resolved Transient Mid-IR Spectroscopy
Authors: Ye Man-ping , Li Heng , Zhang Qing-li , Weng Yu-xiang , Qiu Xiang-gang
Published: September 2007

Carboxyl (COO) vibrational modes of two amino acids histidine and glycine in D2O solution were investigated by temperature-dependent FTIR spectroscopy and temperature-jump nanosecond time-resolved IR difference absorbance spectroscopy. The results show that hydrogen bonds are formed between amino acid molecules as well as between the amino acid molecule and the solvent molecules. The asymmetric vibrational frequency of COO around 1600-1610 cm1 is blue shifted when raising temperature, indicating that the strength of the hydrogen bonds becomes weaker at higher temperature. Two bleaching peaks at 1604 and 1612 cm1 were observed for histidine in response to a temperature jump from 10 C to 20 C. The lower vibrational frequency at 1604 cm1 is assigned to the chain COO group which forms the intermolecular hydrogen bond with {NH3}+ group, while the higher frequency at 1612 cm1 is assigned to the end COO group forming hydrogen bonds with the solvent molecules. This is because that the hydrogen bonds in the former are expected to be stronger than the latter. In addition the intensities of these two bleaching peaks are almost the same. In contrast, only the lower frequency at 1604 cm1 bleaching peak has been observed for glycine. The fact indicates that histidine molecules form a dimer-like intermolecular chain while glycine forms a relatively longer chain in the solution. The rising phase of the IR absorption kinetics in response to the temperature-jump detected at 1604 cm1 for histidine is about 3010 ns, within the resolution limit of our instrument, indicating that breaking or weakening the hydrogen bond is a very fast process.
Characterizing and Manipulating Individual Molecules by Scanning Tunneling Microscopy
Authors: Li Bin , Hou Jian-guo
Published: September 2007

Scanning tunneling microscopy (STM) can provide us the special means to characterize the locally physical and chemical properties of individual molecules, and even help us to manipulate the individual molecules for constructing new molecule-scale devices. Here we have adopted two new types of STM techniques to characterize the encapsulated metal atom inside a fullerene cage, and to construct a molecule-device with strong Kondo effect, respectively. The spatially dI/dV mapping spectra were used to unveil the energy-resolved metal-cage hybrid states of individual Dy@C82 molecule, and the important information about the spatial position of Dy atom inside the cage and the Dy-cage interaction was revealed. The high voltage pulse by STM tip was controlled to induce the dehydrogenation of Co phthalocyanine molecule and change its adsorption configuration on Au(111) surface, so as to recover Kondo effect that disappears in the case of intact adsorbed molecule.
Quantum Dot Based on Z-shaped Graphene Nanoribbon: First-principles Study
Authors: Ren Hao , Li Qun-xiang , Shi Qin-wei , Yang Jin-long
Published: September 2007

The electronic and transport properties of the Z-shaped graphene nanoribbons heterojunction are investigated by a fully self-consistent non-equilibrium Green's function method combined with density functional theory. The first-principles calculations show that the robust quantum confinement effect in the junction can be used to design the quantum dot. The electronic states are confined by the topological structure of the junction. This kind of Z-shaped quantum dot can be realized regardless of doping impurity, edge chemical modification, and the length of junction. Moreover, the spatial distribution and the number of confined states are tunable.
Tunable Photoluminescence of CdTe Nanocrystals over Wide Spectral Range via Microwave-assisted Surface Modification
Authors: Liu Bin , Li Jun , Li Jing-hong
Published: September 2007

An easy and fast microwave-assisted method of tuning the photoluminescence properties of CdTe nanocrystals in aqueous phase is presented. The photoluminescence could be tuned covering almost the whole visual spectral range (537-680 nm), and even partially extending to the near-infrared spectral range. The effect is probably related to the formation of core/shell structure and complex nano-assemblies. These results provide a promising means of tuning the photoluminescence of CdTe nanocrystals, leading to potential applications in biomedical labeling, solar cells, lasers, and other fields.
Construction of an open-access database that integrates cross-reference information from the transcriptome and proteome of immune cells
Authors: Hijikata Atsushi , Kitamura Hiroshi , Kimura Yayoi , Yokoyama Ryo , Aiba Yuichi , Bao Yanyuan , Fujita Shigeharu , Hase Koji , Hori Shohei , Ishii Yasuyuki , Kanagawa Osami , Kawamoto Hiroshi , Kawano Kazuya , Koseki Haruhiko , Kubo Masato , Kurita-Miki Ai , Kurosaki Tomohiro , Masuda Kyoko , Nakata Mitsumasa , Oboki Keisuke , Ohno Hiroshi , Okamoto Mariko , Okayama Yoshimichi , O-Wang Jiyang , Saito Hirohisa , Saito Takashi , Sakuma Machie , Sato Katsuaki , Sato Kaori , Seino Ken-ichiro , Setoguchi Ruka , Tamura Yuki , Tanaka Masato , Taniguchi Masaru , Taniuchi Ichiro , Teng Annabelle , Watanabe Takeshi , Watarai Hiroshi , Yamasaki Sho , Ohara Osamu
Published: September 2007

Motivation: Although a huge amount of mammalian genomic data does become publicly available, there are still hurdles for biologists to overcome before such data can be fully exploited. One of the challenges for gaining biological insight from genomic data has been the inability to cross-reference transcriptomic and proteomic data using a single informational platform. To address this, we constructed an open-access database that enabled us to cross-reference transcriptomic and proteomic data obtained from immune cells.

Results: The database, named RefDIC (Reference genomics Database of Immune Cells), currently contains: (i) quantitative mRNA profiles for human and mouse immune cells/tissues obtained using Affymetrix GeneChip technology; (ii) quantitative protein profiles for mouse immune cells obtained using two-dimensional gel electrophoresis (2-DE) followed by image analysis and mass spectrometry and (iii) various visualization tools to cross-reference the mRNA and protein profiles of immune cells. RefDIC is the first open-access database for immunogenomics and serves as an important information-sharing platform, enabling a focused genomic approach in immunology.

Availability: All raw data and information can be accessed from http://refdic.rcai.riken.jp/. The microarray data is also available at http://cibex.nig.ac.jp/ under CIBEX accession no. CBX19, and http://www.ebi.ac.uk/pride/ under PRIDE accession numbers 2354–2378 and 2414.

Contact:  hijikata@rcai.riken.jp

Supplementary information: Supplementary data are available at Bioinformatics online.
Efficient parameter estimation for spatio-temporal models of pattern formation: case study ofDrosophila melanogaster
Authors: Fomekong-Nanfack Yves , Kaandorp Jaap A. , Blom Joke
Published: September 2007

Motivation: Diffusable and non-diffusable gene products play a major role in body plan formation. A quantitative understanding of the spatio-temporal patterns formed in body plan formation, by using simulation models is an important addition to experimental observation. The inverse modelling approach consists of describing the body plan formation by a rule-based model, and fitting the model parameters to real observed data. In body plan formation, the data are usually obtained from fluorescent immunohistochemistry or in situ hybridizations. Inferring model parameters by comparing such data to those from simulation is a major computational bottleneck. An important aspect in this process is the choice of method used for parameter estimation. When no information on parameters is available, parameter estimation is mostly done by means of heuristic algorithms.

Results: We show that parameter estimation for pattern formation models can be efficiently performed using an evolution strategy (ES). As a case study we use a quantitative spatio-temporal model of the regulatory network for early development in Drosophila melanogaster. In order to estimate the parameters, the simulated results are compared to a time series of gene products involved in the network obtained with immunohistochemistry. We demonstrate that a (μ,λ)-ES can be used to find good quality solutions in the parameter estimation. We also show that an ES with multiple populations is 5–140 times as fast as parallel simulated annealing for this case study, and that combining ES with a local search results in an efficient parameter estimation method.

Supplementary information and availability:  Bioinformatics online; software: http://www.science.uva.nl/research/scs/3D-RegNet/fly_ea

Contact:  jaapk@science.uva.nl
Extending assembly of short DNA sequences to handle error
Authors: Jeck William R. , Reinhardt Josephine A. , Baltrus David A. , Hickenbotham Matthew T. , Magrini Vincent , Mardis Elaine R. , Dangl Jeffery L. , Jones Corbin D.
Published: September 2007

Inexpensive de novo genome sequencing, particularly in organisms with small genomes, is now possible using several new sequencing technologies. Some of these technologies such as that from Illumina's Solexa Sequencing, produce high genomic coverage by generating a very large number of small reads (∼30 bp). While prior work shows that partial assembly can be performed by k-mer extension in error-free reads, this algorithm is unsuccessful with the sequencing error rates found in practice. We present VCAKE (Verified Consensus Assembly by K-mer Extension), a modification of simple k-mer extension that overcomes error by using high depth coverage. Though it is a simple modification of a previous approach, we show significant improvements in assembly results on simulated and experimental datasets that include error.

Availability:  http://152.2.15.114/~labweb/VCAKE

Contact:  william.jeck@gmail.com
Spatial and temporal episodic memory retrieval recruit dissociable functional networks in the human brain
Authors: Ekstrom Arne D. , Bookheimer Susan Y.
Published: September 2007

Imaging, electrophysiological studies, and lesion work have shown that the medial temporal lobe (MTL) is important for episodic memory; however, it is unclear whether different MTL regions support the spatial, temporal, and item elements of episodic memory. In this study we used fMRI to examine retrieval performance emphasizing different aspects of episodic memory in the context of a spatial navigation paradigm. Subjects played a taxi-driver game (“yellowcab”), in which they freely searched for passengers and delivered them to specific landmark stores. Subjects then underwent fMRI scanning as they retrieved landmarks, spatial, and temporal associations from their navigational experience in three separate runs. Consistent with previous findings on item memory, perirhinal cortex activated most strongly during landmark retrieval compared with spatial or temporal source information retrieval. Both hippocampus and parahippocampal cortex activated significantly during retrieval of landmarks, spatial associations, and temporal order. We found, however, a significant dissociation between hippocampal and parahippocampal cortex activations, with spatial retrieval leading to greater parahippocampal activation compared with hippocampus and temporal order retrieval leading to greater hippocampal activation compared with parahippocampal cortex. Our results, coupled with previous findings, demonstrate that the hippocampus and parahippocampal cortex are preferentially recruited during temporal order and spatial association retrieval—key components of episodic “source” memory.
DNA Barcoding is not enough: mismatch of taxonomy and genealogy in New Zealand grasshoppers (Orthoptera: Acrididae).
Authors: Trewick Steven A.
Published: September 2007

DNA barcoding has been touted as a program that will efficiently and relatively cheaply inform on biological diversity; yet many exemplars purporting to demonstrate the efficacy of the method have been undertaken by its principal proponents. Critics of DNA barcoding identify insufficient within‐taxon sampling coupled with the knowledge that levels of haplotypic paraphyly are rather high as key reasons to be sceptical of the value of an exclusively DNA‐based taxonomic. Here I applied a DNA barcoding approach using mtDNA sequences from the cytochrome oxidase I gene to examine diversity in a group of endemic New Zealand grasshoppers belonging to the genus Sigaus. The mtDNA data revealed high genetic distances among individuals of a single morpho‐species, but this diversity was geographically partitioned. Phylogenetic analysis supported at least four haplogroups within one species (Sigaus australis) but paraphyly of this species with respect to several others. In some instances two morphologically and ecologically distinct species shared identical mtDNA haplotypes. The mismatch of genealogy and taxonomy revealed in the Sigaus australis complex indicates that, if used in isolation, DNA barcoding data can be highly misleading about biodiversity. Furthermore, failure to take into account evidence from natural history and morphology when utilizing DNA barcoding will tend to conceal the underlying evolutionary processes associated with speciation.

© The Willi Hennig Society 2007.
Ribosomal DNA pseudogenes are widespread in the eucalypt group (Myrtaceae): implications for phylogenetic analysis
Authors: Bayly Michael J. , Udovicic Frank , Gibbs Adele K. , Parra‐O. Carlos , Ladiges Pauline Y.
Published: September 2007

Pseudogenes from the 18S−5.8S−26S cistron of nuclear ribosomal DNA are reported in the eucalypt group (Myrtaceae), which includes seven genera. Putative pseudogenes are identified by a range of sequence comparisons including: the number of CpG and CpNpG methylation sites, GC content, estimated secondary structure stability of internal transcribed spacer transcripts, the presence of conserved motifs, patterns of sequence relationships and inferred substitution patterns. These comparisons indicate that pseudogenes are widespread, being evident in Eucalyptus (subgenera Eucalyptus and Eudesmia), Corymbia (extracodical sections Rufaria, Ochraria and Blakearia), Angophora, Stockwellia quadrifida and Arillastrum gummiferum. At least six sequences used in previous phylogenetic studies are identified as pseudogenes, and a further 10 pseudogenes are newly sequenced here. Gene trees place pseudogenes in a number of distinct lineages: pseudogenes from Eucalyptus group with other Eucalyptus sequences, those from Corymbia and Angophora group with other Corymbia/Angophora sequences, that from Stockwellia groups with other sequences from the Eucalyptopsis group, and that from Arillastrum is placed as sister to the other included sequence of Arillastrum. Some pseudogenes in Eucalyptus, Corymbia and Angophora represent “deep” ribosomal DNA paralogues that pre‐date species differentiation in these groups, and a recombination analysis shows no evidence of recombination between putative pseudogenes and their functional counterparts. The presence of divergent paralogues presents both challenges and opportunities for the reconstruction of eucalypt phylogenies using ribosomal DNA sequences. Phylogenetic data sets should include only orthologous sequences, but different paralogues potentially provide additional, independent, character sets for phylogenetic analyses.

© The Willi Hennig Society 2007.
The chili pepper CaATL1: an AT‐hook motif‐containing transcription factor implicated in defence responses against pathogens
Authors: KIM SOO‐YONG , KIM YOUNG‐CHEOL , SEONG EUN SOO , LEE YONG‐HWAN , PARK JEONG MEE , CHOI DOIL
Published: September 2007

Using cDNA microarray analysis, we isolated a cDNA clone,CaATL1(Capsicum annuumL. BukangAT‐hook‐Likegene1), from a chili pepper plant incompatibly interacting with bacterial pathogens. The deduced amino acid sequence has a potential nuclear localization sequence and an AT‐hook DNA binding motif which can bind AT‐rich sequence elements. Expression ofCaATL1was specifically induced in host‐ and non‐host‐resistant responses against bacterial and viral pathogens in pepper plants. In addition,CaATL1transcripts also increased following salicylic acid and ethephone treatment but were only mildly induced by methyl‐jasmonate treatment. CaATL1::smGFP (soluble‐modified green fluorescent protein) fusion protein localized to nuclei in tobacco BY2 protoplasts. The C‐terminal region of the CaATL1 protein fused to the LexA DNA binding domain was able to activate reporter gene expression in yeast. To analyse further the role of theCaATL1in pathogen defence response, we generatedCaATL1‐over‐expressing transgenic tomato plants. These transgenic plants showed enhanced disease resistance against bacterial and oomycete pathogens. Taken together, these results provide the first evidence of a role for a plant AT‐hook motif‐containing transcription factor in pathogen defence response.
Aspergillus flavus: the major producer of aflatoxin
Authors: KLICH MAREN A.
Published: September 2007

Aspergillus flavus is an opportunistic pathogen of crops. It is important because it produces aflatoxin as a secondary metabolite in the seeds of a number of crops both before and after harvest. Aflatoxin is a potent carcinogen that is highly regulated in most countries. In the field, aflatoxin is associated with drought‐stressed oilseed crops including maize, peanut, cottonseed and tree nuts. Under the right conditions, the fungus will grow and produce aflatoxin in almost any stored crop seed. In storage, aflatoxin can be controlled by maintaining available moisture at levels below that which will support growth of A. flavus. A number of field control measures are being utilized or explored, including: modification of cultural practices; development of resistant crops through molecular and proteomic techniques; competitive exclusion using strains that do not produce aflatoxin; and development of field treatments that would block aflatoxin production.

Taxonomy:  Aspergillus flavus Link (teleomorph unknown) kingdom Fungi, phyllum Ascomycota, order Eurotiales, class Eurotiomycetes, family Trichocomaceae, genus Aspergillus, species flavus.

Host range:  Aspergillus flavus has a broad host range as an opportunistic pathogen/saprobe. It is an extremely common soil fungus. The major concern with this fungus in agriculture is that it produces highly carcinogenic toxins called aflatoxins which are a health hazard to animals. In the field, A. flavus is predominantly a problem in the oilseed crops maize, peanuts, cottonseed and tree nuts. Under improper storage conditions, A. flavus is capable of growing and forming aflatoxin in almost any crop seed. It also is a pathogen of animals and insects. In humans it is predominantly an opportunistic pathogen of immunosuppressed patients.

Useful websites:  http://www.aspergillusflavus.org, http://www.aflatoxin.info/health.asp, plantpathology.tamu.edu/aflatoxin, http://www.aspergillus.org.uk
Abscisic acid deficiency leads to rapid activation of tomato defence responses upon infection with Erwinia chrysanthemi
Authors: ASSELBERGH BOB , ACHUO ANDREW ENOW , HÖFTE MONICA , VAN GIJSEGEM FRÉDÉRIQUE
Published: September 2007

In addition to the important role of abscisic acid (ABA) in abiotic stress signalling, basal and high ABA levels appear to have a negative effect on disease resistance. Using the ABA‐deficient sitiens tomato (Solanum lycopersicum) mutant and different application methods of exogenous ABA, we demonstrated the influence of this plant hormone on disease progression of Erwinia chrysanthemi. This necrotrophic plant pathogenic bacterium is responsible for soft rot disease on many plant species, causing maceration symptoms mainly due to the production and secretion of pectinolytic enzymes. On wild‐type (WT) tomato cv. Moneymaker E. chrysanthemi leaf inoculation resulted in maceration both within and beyond the infiltrated zone of the leaf, but sitiens showed a very low occurrence of tissue maceration, which never extended the infiltrated zone. A single ABA treatment prior to infection eliminated the effect of pathogen restriction in sitiens, while repeated ABA spraying during plant development rendered both WT and sitiens very susceptible. Quantification of E. chrysanthemi populations inside the leaf did not reveal differences in bacterial growth between sitiens and WT. Sitiens was not more resistant to pectinolytic cell‐wall degradation, but upon infection it showed a faster and stronger activation of defence responses than WT, such as hydrogen peroxide accumulation, peroxidase activation and cell‐wall fortifications. Moreover, the rapid activation of sitiens peroxidases was also observed after application of bacteria‐free culture filtrate containing E. chrysanthemi cell‐wall‐degrading enzymes and was absent during infection with an out E. chrysanthemi mutant impaired in secretion of these extracellular enzymes.
Community ecology of African reptiles: historical perspective and a meta‐analysis using null models
Authors: Luiselli Luca
Published: September 2007

Community ecology and resource‐partitioning patterns of African reptiles have been increasingly studied over the past 30 years. In this paper, I review these studies and provide a meta‐analysis based on null models and Monte Carlo simulations (RA2 and RA3 algorithms) to compare patterns of resource partitioning among reptiles in tropical versus nontropical Africa. In general, studies on community ecology of African reptiles have had a strong impact on the global study of resource‐partitioning patterns in ectotherms, with such authors as Robert Barbault and Eric Pianka being among the most famous having ever worked in Africa. Despite previous claims, in this paper I suggest that there is no true evidence that reptile biomass is depressed in tropical Africa in comparison with tropical regions of other continents. My null‐model reanalysis of 32 independent study systems (twenty from tropical Africa and twelve from nontropical Africa) shows that resource‐partitioning patterns are nearly always found in tropical assemblages of reptiles, although this cannot be said for nontropical assemblages of species. Microhabitat (especially for lizards) and food (especially for snakes) are the resource axes typically partitioned by African reptiles.
The Riyadh Intensive Care Program mortality prediction algorithm assessed in 617 intensive care patients in Glasgow
Authors: HOPE A. T. , PLENDERLEITH J. L.
Published: September 2007

The hospital mortality prediction algorithm from the Riyadh Intensive Care Program was assessed in 617 general intensive care unit patients and the results were compared with APACHE II admission scoring. Of the 119 patients predicted to die by the Riyadh Intensive Care Program, 24 (20.2%) recovered sufficiently to be discharged home. The overall false‐positive rate was 5.2%, the false predictions mostly occurring in the trended component, the admission component having similar performance to admission APACHE II. For equivalent specificity the Riyadh Intensive Care Program was more sensitive than admission APACHE II risk of death figures, but the very high false‐positive rate in those predicted to die precludes the algorithm's use in patient management decisions. In our view, the Riyadh Intensive Care Program does not justify the considerable extra work involved in data collection and processing over current admission scoring systems.
Haemodynamic and plasma catecholamine responses during total intravenous anaesthesia for laryngomicroscopy
Authors: MUSTOLA S. T. , BAER G. A. , METSÄ‐KETELÄ T. , LAIPPALA P.
Published: September 2007

We compared the haemodynamic responses to endolaryngeal procedures during anaesthesia with propofol or thiopentone. Two minutes after administration of glycopyrronium 4μg.kg‐1 and alfentanil 17.5 μg.kg‐1 anaesthesia was induced with either propofol 2.0mg.kg ‐1 (n = 8) or thiopentone 5.0mg.kg ‐1 (n = 8) by random allocation and maintained with a fixed rate infusion of propofol 0.2mg.kg‐1.min‐1 or thiopentone 0.3mg.kg‐1.min‐1, respectively. Muscle relaxation was induced and maintained with suxamethonium. Intratracheal jet‐ventilation (rate: 20 breath.min‐1) was with 100% oxygen. Blood samples for later determination of plasma catecholamines were drawn and haemodynamic responses were recorded at tracheal intubation, after insertion of the operating laryngoscope, during the endolaryngeal procedure and after extubation. With both anaesthetic agents the only statistically significant haemodynamic response to intubation was a rise of heart rate. With propofol, plasma adrenaline concentrations decreased significantly after induction and remained below baseline values throughout the procedure. After insertion of the operating laryngoscope the haemodynamic response was more pronounced with thiopentone than with propofol. Propofol blocks the catecholamine and haemodynamic responses to endolaryngeal procedures more effectively than thiopentone.
Gastric emptying in patients the day after cardiac surgery
Authors: GOLDHILL D. R. , WHELPTON R. , WINYARD J. A. , WILKINSON K. A.
Published: September 2007

Fourteen adults underwent cardiac surgery with a standard anaesthetic technique. Prior to surgery and the day after surgery, gastric emptying was determined using the paracetamol absorption technique. Results from 13 patients were available for analysis. The mean time to reach the maximum plasma concentration was 14.1 min (SEM 2.1)pre–operatively and 225.4min (SEM 42.3) postoperatively. The mean maximum concentration was 23.7mg l‐1 (SEM 1.9) pre–operatively and 5.1mg.l‐1 (SEM 0.8) postoperatively. The area under the curve (0–60 min) was 892 mg min.I ‐1 (SEM 57) pre –operatively and 131 mg min‐1 (SEM 25) postoperatively. The differences between pre– and postoperative values were highly significant for all these three measurements. We conclude that gastric emptying is markedly delayed the day after elective cardiac surgery.
Changes in intra–ocular pressure during general anaesthesia
Authors: MYINT Y. , SINGH A. K. , PEACOCK J. E. , PADFIELD A.
Published: September 2007

Changes in intra–ocular pressure during spontaneous ventilation with a laryngeal mask were compared with controlled ventilation using a tracheal tube in 40 patients undergoing intra–ocular surgery under general anaesthesia. Intra–ocular pressure was measured before induction, after establishing the airway, at the end of the operation and after removal of the airway device. Anaesthesia was induced with propofol and maintained with enflurane and nitrous oxide in oxygen. Mean end–tidal carbon dioxide tension was significantly higher during spontaneous ventilation than during controlled ventilation 5min after establishing the airway (5.7 versus 4.5) and at the end of surgery (6.1 versus 4.2) (p < 0.001). Despite this, intra–ocular pressures were lower than baseline and similar in the two groups throughout anaesthesia. At the end of surgery, intra–ocular pressure (mmHg) was 11.2 and 8.6 during spontaneous or controlled ventilation respectively. One min after removal of the device, mean intra–ocular pressure (mmHg) in the tracheal tube group (16.0) was slightly higher than baseline (15.3) and was significantly higher than the laryngeal mask group (10.9) (p < 0.01). Spontaneous ventilation with a laryngeal mask is an acceptable alternative to controlled ventilation with tracheal intubation in elective intra–ocular surgery.
A new device for measuring and recording the forces applied during laryngoscopy
Authors: McCOY É. P. , AUSTIN B. A. , MIRAKHUR R. K. , WONG K. C.
Published: September 2007

In characterising the forces exerted during laryngoscopy it is accepted that the significant force component is that which is parallel to the axis of the laryngoscope handle. This paper describes a new method of evaluating the forces exerted at laryngoscopy. A laryngoscope handle has been redesigned, incorporating a force‐displacement transducer on the handle at the end opposite to where the blade is attached. The device is designed specifically to sense the axial component of force. The blade attachment block has been detached from the sleeve and connected to a steel shaft which forms the new battery compartment. This allows the axial force exerted at the blade during laryngoscopy to be transmitted along this shaft to the sensing transducer. Linear ball bearings have been introduced between the new shaft and the handle sleeve (outer casing). The rolling friction has been reduced to less than 0.1 % by diamond‐lapping the precision ground surface ‐hardened rod to produce a mirror finish. Thus, the force transmitted to the transducer is essentially constant regardless of where the load is applied along the blade. The output from the system is directly downloaded to a laptop computer and the data analysed almost instantaneously to determine the duration of laryngoscopy, the peak forces applied, the mean force with its standard deviation and graphic display of the data. Provision has been made for data entry checks, recording patient details and study data, and creating a data base for the storage and retrieval of the study details.
Use of a modified occlusal bite guard to prevent self‐induced injury in intensive care patients
Authors: ROBERTS G. J.
Published: September 2007

The use of a simple bite raiser is usually effective in preventing self‐inflicted tongue and lip trauma. In some patients with very severe uncontrolled muscular activity, this is insufficient. To overcome these problems it is necessary to use a modified bite raiser which prevents the jaws occluding. Such a modified bite raiser is described.
High frequency jet ventilation for severe haemoptysis during extracorporeal circulation
Authors: Jongh R. De , Vundelinckx G. , Schroë H. , Heylen R.
Published: September 2007

Two patients are described in whom fulminant haemoptysis occurred during extracorporeal circulation. The use of high frequency jet ventilation resulted in a dramatic decrease of blood loss from the tracheal tube, avoiding the need for more aggressive management.
Management of life threatening adult postpneumonectomy syndrome
Authors: Evans G.H. , Clark R.J.
Published: September 2007

A case of life threatening airway obstruction secondary to bronchial compression following right pneumonectomy is reported. The aetiology of postpneumonectomy syndrome and the anaesthetic dilemmas faced are discussed with reference to the adaptation and use of a chest drain tube as an improvised airway to bypass the bronchial obstruction.