bluuebunny/crossref_metadata_2025 huggingface dataset:
Ring waveguide resonator on surface acoustic waves: First experiments
Authors: Biryukov S. V. , Schmidt H. , Sotnikov A. V. , Weihnacht M. , Chemekova T. Yu. , Makarov Yu. N.
Published: December 2009

First results of numerical and physical experiments for the ring waveguide resonator on surface acoustic waves are presented. The structure consists of a gold interdigital transducer in the form of a ring placed on the Z cut of aluminum nitride crystal. Excitation of radial modes is investigated. The electrical admittance frequency dependence of such resonator does not have sidelobes. A high quality factor is achievable.
Low-frequency vibrational properties of lysozyme in sugar aqueous solutions: A Raman scattering and molecular dynamics simulation study
Authors: Lerbret A. , Affouard F. , Bordat P. , Hédoux A. , Guinet Y. , Descamps M.
Published: December 2009

The low-frequency (ω<400 cm−1) vibrational properties of lysozyme in aqueous solutions of three well-known protecting sugars, namely, trehalose, maltose, and sucrose, have been investigated by means of complementary Raman scattering experiments and molecular dynamics simulations. The comparison of the Raman susceptibility χ″(ω) of lysozyme/water and lysozyme/sugar/water solutions at a concentration of 40 wt % with the χ″ of dry lysozyme suggests that the protein dynamics mostly appears in the broad peak around 60–80 cm−1 that reflects the vibrations experienced by atoms within the cage formed by their neighbors, whereas the broad shoulder around 170 cm−1 mainly stems from the intermolecular O–H⋯O stretching vibrations of water. The addition of sugars essentially induces a significant high frequency shift and intensity reduction of this band that reveal a slowing down of water dynamics and a distortion of the tetrahedral hydrogen bond network of water, respectively. Furthermore, the lysozyme vibrational densities of states (VDOS) have been determined from simulations of lysozyme in 37–60 wt % disaccharide aqueous solutions. They exhibit an additional broad peak around 290 cm−1, in line with the VDOS of globular proteins obtained in neutron scattering experiments. The influence of sugars on the computed VDOS mostly appears on the first peak as a slight high-frequency shift and intensity reduction in the low-frequency range (ω<50 cm−1), which increase with the sugar concentration and with the exposition of protein residues to the solvent. These results suggest that sugars stiffen the environment experienced by lysozyme atoms, thereby counteracting the softening of protein vibrational modes upon denaturation, observed at high temperature in the Raman susceptibility of the lysozyme/water solution and in the computed VDOS of unfolded lysozyme in water. Finally, the Raman susceptibility of sugar/water solutions and the calculated VDOS of water in the different lysozyme solutions confirm that sugars induce a significant strengthening of the hydrogen bond network of water that may stabilize proteins at high temperatures.
Structure and dynamics of dilute suspensions of finite-Reynolds-number settling fibers
Authors: Shin Mansoo , Koch Donald L. , Subramanian Ganesh
Published: December 2009

Many-fiber simulations and a linear stability analysis are used to explore the structure and dynamics that arise in a dilute suspension of sedimenting slender fibers with finite particle Reynolds numbers. Dynamic simulations based on a slender-body treatment of the fibers coupled with a pseudospectral solution of the Navier–Stokes equations reveal an inhomogeneous structure dominated by the largest wavelength that fits in the periodic simulation cell. This structure becomes weaker with increasing fiber Reynolds number and fiber concentration. A linear stability analysis shows that the stability of the homogeneous state of the suspension is determined by the direction of the horizontal migration of a fiber in a weak shear field with vertical streamlines produced by a perturbation to the fiber number density. The lift force on a settling fiber, in a plane transverse to gravity, has two contributions. The first contribution results from a broken symmetry in the presence of shear at finite Reynolds number, and involves the coupled effects of the shear and translational inertial terms. The second contribution is related to the sedimentation-driven drift of an inclined fiber, and is present even in the Stokes limit. Both contributions act to push fibers toward downward flowing, high density regions, and the net transverse drift is therefore of a destabilizing nature. The drift calculation and its implications for the instability of a homogeneous suspension are explored up to a Reynolds number of 10.6. The structure factor, fluid velocity fluctuations, and deviations of the fiber orientation away from the horizontal plane are found to generally decrease with increasing Reynolds number as a result of the increasing dominance of the inertial torque acting to rotate settling fibers toward the horizontal plane.
Partial strain relaxation via misfit dislocation generation at heterointerfaces in (Al,In)GaN epitaxial layers grown on semipolar (112¯2) GaN free standing substrates
Authors: Tyagi Anurag , Wu Feng , Young Erin C. , Chakraborty Arpan , Ohta Hiroaki , Bhat Rajaram , Fujito Kenji , DenBaars Steven P. , Nakamura Shuji , Speck James S.
Published: December 2009

Misfit strain relaxation via misfit dislocation (MD) generation was observed in heteroepitaxially grown (Al,In)GaN layers on free-standing semipolar (112¯2) GaN substrates. Cross-section transmission electron microscope images revealed MD arrays at alloy heterointerfaces, with the MD line direction and Burgers vector parallel to [11¯00] and [112¯0], respectively. The MD structure is consistent with plastic relaxation by dislocation glide on the (0001) plane. Since (0001) is the only slip plane, the plastic relaxation is associated with tilt of the epitaxial (Al,In)GaN layers. The tilt, measured via high-resolution x-ray diffraction, can be used to quantify the relaxation.
Self-ordering mechanism of nanocluster-chain on the functional vicinal surfaces
Authors: Wan Jian-Feng , Carter W. Craig
Published: December 2009

An energy model of nanoclusters-chain self-organized on the functional vicinal surfaces is established to investigate the self-ordering processes, which provides a promising and challenging nanomaterial-design method by means of the energy minimum principle and entropy change principle. The cluster-chain structure can be predicted through controlling the linear coverage of nanoclusters (PM) and the step width (L). The different interactions including the steps and terraces will perform a positive influence on the self-ordering due to their long-range forces.
Study of laser-plasma interaction using a physics-based model for understanding the physical mechanism of double-pulse effect in nanosecond laser ablation
Authors: Wu Benxin , Zhou Yun , Forsman Andrew
Published: December 2009

This paper studies the double-pulse effect in high-intensity (≥∼GW/cm2) nanosecond (ns) laser ablation, which refers to the significant material removal rate enhancement for ablation by two ns laser pulses (often separated by a delay time of ∼10 to 100 ns). The early-stage interaction of the second laser pulse with the plasma plume created by the first pulse is very important for understanding the physical mechanism of the double pulse effect. However, the plasma properties in the early stage (during a laser pulse or within 20 to 30 ns after the completion of the pulse) are very difficult to measure experimentally. In this letter, a physics-based predictive model is used as the investigation tool, which was previously verified based on experiments on plasma properties in the late stage, which are relatively easy to measure. The study shows that the second laser pulse does not directly strike the target condensed phase. Instead, it mainly interacts with the plasma plume created by the first laser pulse, heats and accelerates the ablated material in the plume lingering above the target surface.
Two-color quantum dot laser with tunable wavelength gap
Authors: Li S. G. , Gong Q. , Lao Y. F. , Yang H. D. , Gao S. , Chen P. , Zhang Y. G. , Feng S. L. , Wang H. L.
Published: December 2009

We report on two-color InAs/InP(100) quantum dot lasers with tunable wavelength gap. Two peaks of lasing emission were observed simultaneously, while the high energy peak undergoes continuous blueshift with the increase in the injection current, and the low energy peak is somewhat fixed. Sophisticated studies of the wavelength gap as a function of the laser power prove that the two-peak lasing and shifting is not caused by the effect of Rabi oscillation. Moreover, comparison of electroluminescence and lasing spectra under different injection currents reveal the blueshift of the high energy peak is most likely related to the state-filling effect.
Allelic variation in the Tyk2 and EGF genes as potential genetic determinants of CNS repair
Authors: Bieber Allan J. , Suwansrinon Kanitta , Kerkvliet Jason , Zhang Weidong , Pease Larry R. , Rodriguez Moses
Published: December 2009

The potential for endogenous remyelination and axonal protection can be an important factor in determining disease outcome in demyelinating diseases like multiple sclerosis. In many multiple sclerosis (MS) patients CNS repair fails or is incomplete whereas in others the disease is accompanied by extensive repair of demyelinated lesions. We have described significant differences in the ability of two strains of mice to repair CNS damage following Theiler’s virus-induced demyelination: FVB/NJ (FVB) mice repair damaged myelin spontaneously and completely, whereas B10.D1-H2
q
/SgJ (B10.Q) mice are deficient in the repair process. A QTL analysis was performed to identify genetic loci that differentially regulate CNS repair following chronic demyelination in these strains and two QTL were detected: one on chromosome 3 with a LOD score of 9.3 and a second on chromosome 9 with a LOD score of 14.0. The mouse genes for epidermal growth factor (EGF) and Tyk2 are encoded within the QTL on chromosomes 3 and 9, respectively. Sequence polymorphisms between the FVB and B10.Q strains at both the
EGF
and
Tyk2
loci define functional variations consistent with roles for these genes in regulating myelin repair. EGF is a key regulator of cell growth and development and we show a sevenfold increase in EGF expression in FVB compared to B10.Q mice. Tyk2 is a Janus kinase that plays a central role in controlling the T
H
1 immune response and we show that attenuation of Tyk2 function correlates with enhanced CNS repair.
Engineering the cell wall by reducing de-methyl-esterified homogalacturonan improves saccharification of plant tissues for bioconversion
Authors: Lionetti Vincenzo , Francocci Fedra , Ferrari Simone , Volpi Chiara , Bellincampi Daniela , Galletti Roberta , D’Ovidio Renato , De Lorenzo Giulia , Cervone Felice
Published: December 2009

Plant cell walls represent an abundant, renewable source of biofuel and other useful products. The major bottleneck for the industrial scale-up of their conversion to simple sugars (saccharification), to be subsequently converted by microorganisms into ethanol or other products, is their recalcitrance to enzymatic saccharification. We investigated whether the structure of pectin that embeds the cellulose-hemicellulose network affects the exposure of cellulose to enzymes and consequently the process of saccharification. Reduction of de-methyl-esterified homogalacturonan (HGA) in Arabidopsis plants through the expression of a fungal polygalacturonase (PG) or an inhibitor of pectin methylesterase (PMEI) increased the efficiency of enzymatic saccharification. The improved enzymatic saccharification efficiency observed in transformed plants could also reduce the need for acid pretreatment. Similar results were obtained in PG-expressing tobacco plants and in PMEI-expressing wheat plants, indicating that reduction of de-methyl-esterified HGA may be used in crop species to facilitate the process of biomass saccharification.
Dynein light chain 1 is required for autophagy, protein clearance, and cell death inDrosophila
Authors: Batlevi Yakup , Martin Damali N. , Pandey Udai Bhan , Simon Claudio R. , Powers Christine M. , Taylor J. Paul , Baehrecke Eric H.
Published: December 2009

Autophagy is a catabolic pathway that is important for turnover of long-lived proteins and organelles, and has been implicated in cell survival, tumor progression, protection from infection, neurodegeneration, and cell death. Autophagy and caspases are required for type II autophagic cell death ofDrosophilalarval salivary glands during development, but the mechanisms that regulate these degradation pathways are not understood. We conducted a forward genetic screen for genes that are required for salivary gland cell death, and here we describe the identification ofDrosophila dynein light chain 1(ddlc1) as a gene that is required for type II cell death. Autophagy is attenuated inddlc1mutants, but caspases are active in these cells.ddlc1mutant salivary glands develop large fibrillar protein inclusions that stain positive for amyloid-specific dyes and ubiquitin. Ectopic expression of Atg1 is sufficient to induce autophagy, clear protein inclusions, and rescue degradation ofddlc1mutant salivary glands. Furthermore,ddlc1mutant larvae have decreased motility, and mutations inddlc1enhance the impairment of motility that is observed in aDrosophilamodel of neurodegenerative disease. Significantly, this decrease in larval motility is associated with decreased clearance of protein with polyglutamine expansion, the accumulation of p62 in neurons and muscles, and fewer synaptic boutons. These results indicate that DDLC1 is required for protein clearance by autophagy that is associated with autophagic cell death and neurodegeneration.
Live-cell imaging of photosystem II antenna dissociation during state transitions
Authors: Iwai Masakazu , Yokono Makio , Inada Noriko , Minagawa Jun
Published: December 2009

Plants and green algae maintain efficient photosynthesis under changing light environments by adjusting their light-harvesting capacity. It has been suggested that energy redistribution is brought about by shuttling the light-harvesting antenna complex II (LHCII) between photosystem II (PSII) and photosystem I (PSI) (state transitions), but such molecular remodeling has never been demonstrated in vivo. Here, using chlorophyll fluorescence lifetime imaging microscopy, we visualized phospho-LHCII dissociation from PSII in live cells of the green alga
Chlamydomonas reinhardtii
. Induction of energy redistribution in wild-type cells led to an increase in, and spreading of, a 250-ps lifetime chlorophyll fluorescence component, which was not observed in the
stt7
mutant incapable of state transitions. The 250-ps component was also the dominant component in a mutant containing the light-harvesting antenna complexes but no photosystems. The appearance of the 250-ps component was accompanied by activation of LHCII phosphorylation, supporting the visualization of phospho-LHCII dissociation. Possible implications of the unbound phospho-LHCII on energy dissipation are discussed.
PIN phosphorylation is sufficient to mediate PIN polarity and direct auxin transport
Authors: Zhang Jing , Nodzyński Tomasz , Pěnčík Aleš , Rolčík Jakub , Friml Jiří
Published: December 2009

The plant hormone auxin plays a crucial role in regulating plant development and plant architecture. The directional auxin distribution within tissues depends on PIN transporters that are polarly localized on the plasma membrane. The PIN polarity and the resulting auxin flow directionality are mediated by the antagonistic actions of PINOID kinase and protein phosphatase 2A. However, the contribution of the PIN phosphorylation to the polar PIN sorting is still unclear. Here, we identified an evolutionarily conserved phosphorylation site within the central hydrophilic loop of PIN proteins that is important for the apical and basal polar PIN localizations. Inactivation of the phosphorylation site in PIN1(Ala) resulted in a predominantly basal targeting and increased the auxin flow to the root tip. In contrast, the outcome of the phosphomimic PIN1(Asp) manipulation was a constitutive, PINOID-independent apical targeting of PIN1 and an increased auxin flow in the opposite direction. Furthermore, the PIN1(Asp) functionally replaced PIN2 in its endogenous expression domain, revealing that the phosphorylation-dependent polarity regulation contributes to functional diversification within the PIN family. Our data suggest that PINOID-independent PIN phosphorylation at one single site is adequate to change the PIN polarity and, consequently, to redirect auxin fluxes between cells and provide the conceptual possibility and means to manipulate auxin-dependent plant development and architecture.
T-705 (favipiravir) activity against lethal H5N1 influenza A viruses
Authors: Kiso Maki , Takahashi Kazumi , Sakai-Tagawa Yuko , Shinya Kyoko , Sakabe Saori , Le Quynh Mai , Ozawa Makoto , Furuta Yousuke , Kawaoka Yoshihiro
Published: December 2009

The neuraminidase inhibitors oseltamivir and zanamivi are used to treat H5N1 influenza. However, oseltamivir-resistant H5N1 viruses have been isolated from oseltamivir-treated patients. Moreover, reassortment between H5N1 viruses and oseltamvir-resistant human H1N1 viruses currently circulating could create oseltamivir-resistant H5N1 viruses, rendering the oseltamivir stockpile obsolete. Therefore, there is a need for unique and effective antivirals to combat H5N1 influenza viruses. The investigational drug T-705 (favipiravir; 6-fluoro-3-hydroxy-2-pyrazinecarboxamide) has antiviral activity against seasonal influenza viruses and a mouse-adapted H5N1 influenza virus derived from a benign duck virus. However, its efficacy against highly pathogenic H5N1 viruses, which are substantially more virulent, remains unclear. Here, we demonstrate that T-705 effectively protects mice from lethal infection with oseltamivir-sensitive or -resistant highly pathogenic H5N1 viruses. Furthermore, our biochemical analysis suggests that T-705 ribofuranosyl triphosphate, an active form of T-705, acts like purines or purine nucleosides in human cells and does not inhibit human DNA synthesis. We conclude that T-705 shows promise as a therapeutic agent for the treatment of highly pathogenic H5N1 influenza patients.
Molecular basis of factor IXa recognition by heparin-activated antithrombin revealed by a 1.7-Å structure of the ternary complex
Authors: Johnson Daniel J. D. , Langdown Jonathan , Huntington James A.
Published: December 2009

Factor (f) IXa is a critical enzyme for the formation of stable blood clots, and its deficiency results in hemophilia. The enzyme functions at the confluence of the intrinsic and extrinsic pathways by binding to fVIIIa and rapidly generating fXa. In spite of its importance, little is known about how fIXa recognizes its cofactor, its substrate, or its only known inhibitor, antithrombin (AT). However, it is clear that fIXa requires extensive exosite interactions to present substrates for efficient cleavage. Here we describe the 1.7-Å crystal structure of fIXa in its recognition (Michaelis) complex with heparin-activated AT. It represents the highest resolution structure of both proteins and allows us to address several outstanding issues. The structure reveals why the heparin-induced conformational change in AT is required to permit simultaneous active-site and exosite interactions with fIXa and the nature of these interactions. The reactive center loop of AT has evolved to specifically inhibit fIXa, with a P2 Gly so as not to clash with Tyr99 on fIXa, a P4 Ile to fit snugly into the S4 pocket, and a C-terminal extension to exploit a unique wall-like feature of the active-site cleft. Arg150 is at the center of the exosite interface, interacting with AT residues on β-sheet C. A surprising crystal contact is observed between the heparin pentasaccharide and fIXa, revealing a plausible mode of binding that would allow longer heparin chains to bridge the complex.
Do mycobacteria produce endospores?
Authors: Traag Bjorn A. , Driks Adam , Stragier Patrick , Bitter Wilbert , Broussard Gregory , Hatfull Graham , Chu Frances , Adams Kristin N. , Ramakrishnan Lalita , Losick Richard
Published: December 2009

The genus
Mycobacterium
, which is a member of the high G+C group of Gram-positive bacteria, includes important pathogens, such as
M. tuberculosis
and
M. leprae
. A recent publication in PNAS reported that
M. marinum
and
M. bovis
bacillus Calmette–Guérin produce a type of spore known as an endospore, which had been observed only in the low G+C group of Gram-positive bacteria. Evidence was presented that the spores were similar to endospores in ultrastructure, in heat resistance and in the presence of dipicolinic acid. Here, we report that the genomes of
Mycobacterium
species and those of other high G+C Gram-positive bacteria lack orthologs of many, if not all, highly conserved genes diagnostic of endospore formation in the genomes of low G+C Gram-positive bacteria. We also failed to detect the presence of endospores by light microscopy or by testing for heat-resistant colony-forming units in aged cultures of
M. marinum
. Finally, we failed to recover heat-resistant colony-forming units from frogs chronically infected with
M. marinum
. We conclude that it is unlikely that
Mycobacterium
is capable of endospore formation.
Wolbachia
as a bacteriocyte-associated nutritional mutualist
Authors: Hosokawa Takahiro , Koga Ryuichi , Kikuchi Yoshitomo , Meng Xian-Ying , Fukatsu Takema
Published: December 2009

Many insects are dependent on bacterial symbionts that provide essential nutrients (ex. aphid–
Buchnera
and tsetse–
Wiglesworthia
associations), wherein the symbionts are harbored in specific cells called bacteriocytes that constitute a symbiotic organ bacteriome. Facultative and parasitic bacterial symbionts like
Wolbachia
have been regarded as evolutionarily distinct from such obligate nutritional mutualists. However, we discovered that, in the bedbug
Cimex lectularius
,
Wolbachia
resides in a bacteriome and appears to be an obligate nutritional mutualist. Two bacterial symbionts, a
Wolbachia
strain and an unnamed γ-proteobacterium, were identified from different strains of the bedbug. The
Wolbachia
symbiont was detected from all of the insects examined whereas the γ-proteobacterium was found in a part of them. The
Wolbachia
symbiont was specifically localized in the bacteriomes and vertically transmitted via the somatic stem cell niche of germalia to oocytes, infecting the incipient symbiotic organ at an early stage of the embryogenesis. Elimination of the
Wolbachia
symbiont resulted in retarded growth and sterility of the host insect. These deficiencies were rescued by oral supplementation of B vitamins, confirming the essential nutritional role of the symbiont for the host. The estimated genome size of the
Wolbachia
symbiont was around 1.3 Mb, which was almost equivalent to the genome sizes of parasitic
Wolbachia
strains of other insects. These results indicate that bacteriocyte-associated nutritional mutualism can evolve from facultative and prevalent microbial associates like
Wolbachia
, highlighting a previously unknown aspect of the parasitism-mutualism evolutionary continuum.
The induction of folding cooperativity by ligand binding drives the allosteric response of tetracycline repressor
Authors: Reichheld Sean E. , Yu Zhou , Davidson Alan R.
Published: December 2009

Tetracycline (Tc) repressor (TetR) undergoes an allosteric transition upon interaction with the antibiotic, Tc, that abrogates its ability to specifically bind its operator DNA. In this work, by performing equilibrium protein unfolding experiments on wild-type TetR and mutants displaying altered allosteric responses, we have delineated a model to explain TetR allostery. In the absence of Tc, we show that the DNA-binding domains of this homodimeric protein are relatively flexible and unfold independently of the Tc binding/dimerization (TBD) domains. Once Tc is bound, however, the unfolding of the DNA binding domains becomes coupled to the TBD domains, leading to a large increase in DNA-binding domain stability. Noninducible TetR mutants display considerably less interdomain folding cooperativity upon binding to Tc. We conclude that the thermodynamic coupling of the TetR domains caused by Tc binding and the resulting rigidification of the DNA-binding domains into a conformation that is incompatible with DNA binding are the fundamental factors leading to the allosteric response in TetR. This allosteric mechanism can account for properties of the whole TetR family of repressors and may explain the functioning and evolution of other allosteric systems. Our model contrasts with the prevalent view that TetR populates two distinct conformations and that Tc causes a switch between these defined conformations.
Posttranslational regulation impacts the fate of duplicated genes
Authors: Amoutzias Grigoris D. , He Ying , Gordon Jonathan , Mossialos Dimitris , Oliver Stephen G. , Van de Peer Yves
Published: December 2009

Gene and genome duplications create novel genetic material on which evolution can work and have therefore been recognized as a major source of innovation for many eukaryotic lineages. Following duplication, the most likely fate is gene loss; however, a considerable fraction of duplicated genes survive. Not all genes have the same probability of survival, but it is not fully understood what evolutionary forces determine the pattern of gene retention. Here, we use genome sequence data as well as large-scale phosphoproteomics data from the baker’s yeast
Saccharomyces cerevisiae
, which underwent a whole-genome duplication ∼100 mya, and show that the number of phosphorylation sites on the proteins they encode is a major determinant of gene retention. Protein phosphorylation motifs are short amino acid sequences that are usually embedded within unstructured and rapidly evolving protein regions. Reciprocal loss of those ancestral sites and the gain of new ones are major drivers in the retention of the two surviving duplicates and in their acquisition of distinct functions. This way, small changes in the sequences of unstructured regions in proteins can contribute to the rapid rewiring and adaptation of regulatory networks.
The quorum-quenching
N
-acyl homoserine lactone acylase PvdQ is an Ntn-hydrolase with an unusual substrate-binding pocket
Authors: Bokhove Marcel , Jimenez Pol Nadal , Quax Wim J. , Dijkstra Bauke W.
Published: December 2009

In many Gram-negative pathogens, their virulent behavior is regulated by quorum sensing, in which diffusible signals such as
N
-acyl homoserine lactones (AHLs) act as chemical messaging compounds. Enzymatic degradation of these diffusible signals by, e.g., lactonases or amidohydrolases abolishes AHL regulated virulence, a process known as quorum quenching. Here we report the first crystal structure of an AHL amidohydrolase, the AHL acylase PvdQ from
Pseudomonas aeruginosa
. PvdQ has a typical α/β heterodimeric Ntn-hydrolase fold, similar to penicillin G acylase and cephalosporin acylase. However, it has a distinct, unusually large, hydrophobic binding pocket, ideally suited to recognize C12 fatty acid-like chains of AHLs. Binding of a C12 fatty acid or a 3-oxo-C12 fatty acid induces subtle conformational changes to accommodate the aliphatic chain. Furthermore, the structure of a covalent ester intermediate identifies Serβ1 as the nucleophile and Asnβ269 and Valβ70 as the oxyanion hole residues in the AHL degradation process. Our structures show the versatility of the Ntn-hydrolase scaffold and can serve as a structural paradigm for Ntn-hydrolases with similar substrate preference. Finally, the quorum-quenching capabilities of PvdQ may be utilized to suppress the quorum-sensing machinery of pathogens.
A self-assembling peptide acting as an immune adjuvant
Authors: Rudra Jai S. , Tian Ye F. , Jung Jangwook P. , Collier Joel H.
Published: December 2009

The development of vaccines and other immunotherapies has been complicated by heterogeneous antigen display and the use of incompletely defined immune adjuvants with complex mechanisms of action. We have observed strong antibody responses in mice without the coadministration of any additional adjuvant by noncovalently assembling a T and B cell epitope peptide into nanofibers using a short C-terminal peptide extension. Self-assembling peptides have been explored recently as scaffolds for tissue engineering and regenerative medicine, but our results indicate that these materials may also be useful as chemically defined adjuvants. In physiological conditions, these peptides self-assembled into long, unbranched fibrils that displayed the epitope on their surfaces. IgG1, IgG2a, and IgG3 were raised against epitope-bearing fibrils in levels similar to the epitope peptide delivered in complete Freund’s adjuvant (CFA), and IgM production was even greater for the self-assembled epitope. This response was dependent on self-assembly, and the self-assembling sequence was not immunogenic by itself, even when delivered in CFA. Undetectable levels of interferon-gamma, IL-2, and IL-4 in cultures of peptide-challenged splenocytes from immunized mice suggested that the antibody responses did not involve significant T cell help.
Efficacy of ST-246 versus lethal poxvirus challenge in immunodeficient mice
Authors: Grosenbach Douglas W. , Berhanu Aklile , King David S. , Mosier Stacie , Jones Kevin F. , Jordan Robert A. , Bolken Tove’ C. , Hruby Dennis E.
Published: December 2009

The threat of smallpox as a bioweapon and the emerging threat of human monkeypox, among other poxviral diseases, highlight the need for effective poxvirus countermeasures. ST-246, which targets the F13L protein in vaccinia virus and its homologs in other orthopoxvirus species, provides full protection from lethal poxviral disease in numerous animal models and seems to be safe in humans. All previous evaluations of ST-246 efficacy have been in immunocompetent animals. However, the risk of severe poxviral disease is greater in immunodeficient hosts. Here we report on the efficacy of ST-246 in preventing or treating lethal poxviral disease in immunodeficient mice. After lethal challenge with the Western Reserve strain of vaccinia, Nude, SCID, and JHknockout mice additionally depleted of CD4+and CD8+T cells were not fully protected by ST-246, although survival was significantly extended. However, CD4+T cell deficient, CD8+T cell deficient, JHknockout, and JHknockout mice also deficient for CD4+or CD8+T cells survived lethal challenge when treated with ST-246 starting on the day of challenge. Delaying treatment until 72 h after infection reduced ST-246 efficacy in some models but provided full protection from lethal challenge in most. These findings suggest that ST-246 may be effective in controlling smallpox or other pathogenic orthopoxviruses in some immunodeficient human populations for whom the vaccine is contraindicated.
Regulation of NF-κB by NSD1/FBXL11-dependent reversible lysine methylation of p65
Authors: Lu Tao , Jackson Mark W. , Wang Benlian , Yang Maojing , Chance Mark R. , Miyagi Masaru , Gudkov Andrei V. , Stark George R.
Published: December 2009

NF-κB, a central coordinator of immune and inflammatory responses, must be tightly regulated. We describe a NF-κB regulatory pathway that is driven by reversible lysine methylation of the p65 subunit, carried out by a lysine methylase, the nuclear receptor–binding SET domain-containing protein 1 (NSD1), and a lysine demethylase, F-box and leucine-rich repeat protein 11 (FBXL11). Overexpression of FBXL11 inhibits NF-κB activity, and a high level of NSD1 activates NF-κB and reverses the inhibitory effect of FBXL11, whereas reduced expression of NSD1 decreases NF-κB activation. The targets are K218 and K221 of p65, which are methylated in cells with activated NF-κB. Overexpression of FBXL11 slowed the growth of HT29 cancer cells, whereas shRNA-mediated knockdown had the opposite effect, and these phenotypes were dependent on K218/K221 methylation. In mouse embryo fibroblasts, the activation of most p65-dependent genes relied on K218/K221 methylation. Importantly, expression of the
FBXL11
gene is driven by NF-κB, revealing a negative regulatory feedback loop. We conclude that reversible lysine methylation of NF-κB is an important element in the complex regulation of this key transcription factor.
Immune effectors required for hepatitis B virus clearance
Authors: Yang Priscilla L. , Althage Alana , Chung Josan , Maier Holly , Wieland Stefan , Isogawa Masanori , Chisari Francis V.
Published: December 2009

To better define the mechanism(s) likely responsible for viral clearance during hepatitis B virus (HBV) infection, viral clearance was studied in a panel of immunodeficient mouse strains that were hydrodynamically transfected with a plasmid containing a replication-competent copy of the HBV genome. Neither B cells nor perforin were required to clear the viral DNA transcriptional template from the liver. In contrast, the template persisted for at least 60 days at high levels in NOD/Scid mice and at lower levels in the absence of CD4+and CD8+T cells, NK cells, Fas, IFN-gamma (IFN-γ), IFN-alpha/beta receptor (IFN-α/βR1), and TNF receptor 1 (TNFR1), indicating that each of these effectors was required to eliminate the transcriptional template from the liver. Interestingly, viral replication was ultimately terminated in all lineages except the NOD/Scid mice, suggesting the existence of redundant pathways that inhibit HBV replication. Finally, induction of a CD8+T cell response in these animals depended on the presence of CD4+T cells. These results are consistent with a model in which CD4+T cells serve as master regulators of the adaptive immune response to HBV; CD8+T cells are the key cellular effectors mediating HBV clearance from the liver, apparently by a Fas-dependent, perforin-independent process in which NK cells, IFN-γ, TNFR1, and IFN-α/βR play supporting roles. These results provide insight into the complexity of the systems involved in HBV clearance, and they suggest unique directions for analysis of the mechanism(s) responsible for HBV persistence.
E3 ubiquitin ligase APC/C-Cdh1 accounts for the Warburg effect by linking glycolysis to cell proliferation
Authors: Almeida Angeles , Bolaños Juan P. , Moncada Salvador
Published: December 2009

Cell proliferation is known to be accompanied by activation of glycolysis. We have recently discovered that the glycolysis-promoting enzyme 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, isoform 3 (PFKFB3), is degraded by the E3 ubiquitin ligase APC/C-Cdh1, which also degrades cell-cycle proteins. We now show in two different cell types (neoplastic and nonneoplastic) that both proliferation and aerobic glycolysis are prevented by overexpression of Cdh1 and enhanced by its silencing. Furthermore, we have coexpressed Cdh1 with PFKFB3—either wild-type or a mutant form resistant to ubiquitylation by APC/C-Cdh1—or with the glycolytic enzyme 6-phosphofructo-1-kinase and demonstrated that whereas glycolysis is essential for cell proliferation, its initiation in the presence of active Cdh1 does not result in proliferation. Our experiments indicate that the proliferative response, regardless of whether it occurs in normal or neoplastic cells, is dependent on a decrease in the activity of APC/C-Cdh1, which activates both proliferation and glycolysis. These observations have implications for cell proliferation, neoplastic transformation, and the prevention and treatment of cancer.
GonadSAGE: a comprehensive SAGE database for transcript discovery on male embryonic gonad development
Authors: Lee Tin-Lap , Li Yunmin , Cheung Hoi-Hung , Claus Janek , Singh Sumeeta , Sastry Chandan , Rennert Owen M. , Lau Yun-Fai Chris , Chan Wai-Yee
Published: December 2009

Summary: Serial analysis of gene expression (SAGE) provides an alternative, with additional advantages, to microarray gene expression studies. GonadSAGE is the first publicly available web-based SAGE database on male gonad development that covers six male mouse embryonic gonad stages, including E10.5, E11.5, E12.5, E13.5, E15.5 and E17.5. The sequence coverage of each SAGE library is beyond 150K, ‘which is the most extensive sequence-based male gonadal transcriptome to date’. An interactive web interface with customizable parameters is provided for analyzing male gonad transcriptome information. Furthermore, the data can be visualized and analyzed with the other genomic features in the UCSC genome browser. It represents an integrated platform that leads to a better understanding of male gonad development, and allows discovery of related novel targets and regulatory pathways.

Availability: GonadSAGE is at http://gonadsage.nichd.nih.gov.

Contact:  leetl@mail.nih.gov
Distinct roles for dorsal CA3 and CA1 in memory for sequential nonspatial events
Authors: Farovik Anja , Dupont Laura M. , Eichenbaum Howard
Published: December 2009

Previous studies have suggested that dorsal hippocampal areas CA3 and CA1 are both involved in representing sequences of events that compose unique episodes. However, it is uncertain whether the contribution of CA3 is restricted to spatial information, and it is unclear whether CA1 encodes order per se or contributes by an active maintenance of memories of sequential events. Here, we developed a new behavioral task that examines memory for the order of sequential nonspatial events presented as trial-unique odor pairings. When the interval between odors within a studied pair was brief (3 sec), bilateral dorsal CA3 lesions severely disrupted memory for their order, whereas dorsal CA1 lesions did not affect performance. However, when the inter-item interval was extended to 10 sec, CA1 lesions, as well as CA3 lesions, severely disrupted performance. These findings suggest that the role of CA3 in sequence memory is not limited to spatial information, but rather appears to be a fundamental property of CA3 function. In contrast, CA1 becomes involved when memories for events must be held or sequenced over long intervals. Thus, CA3 and CA1 are both involved in memory for sequential nonspatial events that compose unique experiences, and these areas play different roles that are distinguished by the duration of time that must be bridged between key events.
Method of predicting reference condition biota affects the performance and interpretation of ecological indices
Authors: HAWKINS CHARLES P. , CAO YONG , ROPER BRETT
Published: December 2009

1. The statistical rigour and interpretability of ecological assessments is strongly affected by how well we predict the biological assemblages expected to occur in the absence of human‐caused stress, i.e. the reference condition. In this study, we examined how the specific method used to predict the reference condition affected the performance of two commonly used types of ecological index: RIVPACS‐based O/E indices and multimetric indices (MMIs).

2. These two types of index have generally relied on different approaches to predicting the reference condition. For MMIs, some type of regionalisation is typically used to describe the range of metric values among reference sites and hence the expected range at assessed sites. For O/E indices, continuous modelling is used to predict how the biota varies among sites both among and within regions. Because the prediction method differs for these two types of index, it has been impossible to judge if differences in index performance (accuracy, precision, responsiveness and sensitivity) are caused by differences in the way reference condition biota are predicted or by differences in what the indices measure.

3. We used a common data set of 94 reference sites and 255 managed sites and the same potential set of predictor variables to compare the performance of five different MMIs and three O/E indices that were derived from different prediction methods: null models, multiple linear regression (MLR), classification and regression trees, Random Forests (RF) and linear discriminant functions models (LDM). We then calculated values of these indices for samples collected from the managed catchments as well as samples collected from 13 reference sites that were progressively altered in known ways by a simulation programme.

4. Both the type of predictor used and the type of index affected overall index performance. Modelled indices generally had the greatest sensitivity in assessing managed sites as biologically different from reference. Index sensitivity was determined by both an aspect of index precision (10th percentile of reference condition values) and responsiveness. The O/E indices showed the best scope of response to known biological alteration. All three O/E indices decreased linearly in response to simulated alteration in both overall assemblage structure (Bray‐Curtis dissimilarity) and taxa loss. The MMIs declined linearly from low to intermediate levels of assemblage alteration but were less responsive between intermediate and high levels of biological alteration.

5. Insights gained from simulations can aid in testing assumptions regarding index response to stress and help ensure that we select indices that are ecologically interpretable and most useful to resource managers.
Vascular endocan (ESM‐1) is markedly overexpressed in clear cell renal cell carcinoma
Authors: Leroy Xavier , Aubert Sebastien , Zini Laurent , Franquet Helene , Kervoaze Gwenola , Villers Arnauld , Delehedde Maryse , Copin Marie‐Christine , Lassalle Philippe
Published: December 2009

Leroy X, Aubert S, Zini L, Franquet H, Kervoaze G, Villers A, Delehedde M, Copin M‐C & Lassalle P  (2010) Histopathology56, 180–187

Vascular endocan (ESM‐1) is markedly overexpressed in clear cell renal cell carcinoma

Aims:  In kidney cancer, new anti‐angiogenic therapies have emerged requiring parameters of effectiveness. The aim was to analyse the expression of endocan or endothelial cell‐specific molecule‐1, which is a proteoglycan up‐regulated in presence of pro‐angiogenic factors.

Method and results:  We investigated 44 renal clear cell carcinomas (RCC) and 25 papillary carcinomas (PC). Circulating endocan was detected by enzyme‐linked immunosorbent assays (ELISA) in 14 patients with RCC, in eight with PC and in 15 healthy volunteers. Endocan was detected by immunohistochemistry in endothelial cells in almost all the cases of RCC without immunoreactivity in tumour cells. In PC, only 5/25 tumours exhibited weak immunoreactivity. Reverse transcriptase‐polymerase chain reaction study confirmed that endocan levels were strongly increased in RCC. Endocan was also detected by ELISA at levels from 3‐ to 10‐fold higher in the sera of patients with RCC. In vitro, addition of sunitinib prevented the release of endocan in human umbilical vascular endothelial cells when induced by vascular endothelial growth factor.

Conclusions:  Our results showed that endocan is overexpressed in patients with RCC. Endocan could therefore appear as a marker of interest in the follow‐up and may be a potential parameter to monitor the tumour response to anti‐angiogenic therapeutics.
Gene expression in colorectal neoplasia: modifications induced by tissue ischaemic time and tissue handling protocol
Authors: Bray Susan E , Paulin Fiona E M , Fong Siew Chinn , Baker Lee , Carey Frank A , Levison David A , Steele Robert J C , Kernohan Neil M
Published: December 2009

Bray S E, Paulin F E M, Fong S C, Baker L, Carey F A, Levison D A, Steele R J C & Kernohan N M (2010) Histopathology56, 240–250

Gene expression in colorectal neoplasia: modifications induced by tissue ischaemic time and tissue handling protocol

Aims:  The heterogeneity within individual distinct cancer types in terms of behaviour, response to therapy and prognosis is well recognized. A major goal of translational research projects has therefore been to define clinically significant subgroups of individual tumour types by analysis of mRNA as well as protein expression. An essential premise of such investigations is that expression of these key molecules is a true reflection of conditions present within the neoplastic cells in vivo. The aim was to investigate the effect of methods of tissue handling and storage on expression of mRNA.

Methods and results:  mRNA expression in 60 biopsy samples obtained from 10 patients with colorectal tumours was examined. The mRNA expression profile and the level of expression of specific mRNA species were significantly affected by the procedures used for collection and storage of tissue samples. Significant variation in the level of expression (both increased and decreased) of transcripts was detectable after 15 min, and by 120 min there was a fourfold increase in the number of genes with a more than twofold change in the level of expression.

Conclusions:  Reliable interpretation of results of gene expression at the mRNA level requires standardized protocols for tissue procurement.
A network approach for evaluating and communicating forest change models
Authors: Drescher Michael , Perera Ajith H.
Published: December 2009

1. Knowledge of forest change is often formalized in state‐and‐transition models (STMs). These models generate forecasts of forest condition that are widely used for forest management planning. Common techniques for evaluating such models are complex, requiring specialized skills not available to non‐modellers. Consequently, model transparency can be limited, hampering collaborative resource modelling that otherwise may increase the chances of management success.

2. We demonstrate evaluation of STMs through network visualization that produces intuitively accessible results, comparable to results of more commonly applied, complex techniques. To evaluate this approach, we statistically test model similarities with empirical data. As examples, we use STMs of forest change, alternately parameterized with information from experts and literature, and compare them to our empirical reference information.

3. Graph theoretical analyses revealed differences in structure and dynamics between alternate STMs. For example, compared to empirical STMs, expert STMs were less complex while literature STMs were more complex. Overall, expert STMs were less similar to empirical STMs than were literature STMs, suggesting information in the expert STMs may deviate more strongly from empirical reference data.

4. We used several techniques that provided complementary information, which produced a comprehensive view of network similarity. We speculate that differences between expert and empirical STMs result from lower complexity of mental models compared to empirical data. While we illustrated our approach using a simple matrix model, it could be adapted for more complex STMs. Improvements of the proposed approach could involve representation of forest change rates with waiting times depicted by multigraphs.

5.
Synthesis and applications. Common evaluations of forest change STMs involve complex techniques not easily accessible to non‐modellers. Approaching such models as networks makes their evaluation and statistical testing intuitively accessible to many audiences. Benefits of this approach to modellers include improved communication about models with non‐modellers, while benefits to stakeholders and decision makers include enhanced understanding of models. This may aid a collaborative resource modelling process and should improve the chances of successful resource management plan implementation. While we used an example from boreal forests, our approach could be applied to many other vegetation types globally.