bluuebunny/crossref_metadata_2025 huggingface dataset:
Reduce the start current of Smith-Purcell backward wave oscillator by sidewall grating
Authors: Li D. , Imasaki K. , Gao X. , Yang Z. , Park Gun-Sik
Published: November 2007

A sidewall grating for the Smith-Purcell device is proposed to enhance the coupling of the optical mode with the electron beam and, consequently, relax the stringent requirements to the electron beam. With the help of three-dimensional particle-in-cell simulations, it has been shown that, comparing with the general grating, the usage of a sidewall grating improves the growth rate and dramatically shortens the time for the device to reach saturation. It is also found that the sidewall grating holds the potential to reduce the start current for the operation of a Smith-Purcell backward wave oscillator.
Second harmonic generation of 2.6W green light with thermoelectrically oxidized undoped congruent lithium niobate crystals below 100°C
Authors: Breunig Ingo , Falk Matthias , Knabe Bastian , Sowade Rosita , Buse Karsten , Rabiei Payam , Jundt Dieter H.
Published: November 2007

We demonstrate that thermoelectric oxidization suppresses unwanted light-induced refractive index changes in undoped congruent periodically poled lithium niobate crystals used for single-pass continuous-wave frequency doubling of 1030nm light. The maximum second harmonic output power shows a strong dependence on the phase matching temperature. For 90°C, a total of 2.6W green light is generated with an efficiency of 22% corresponding to a normalized conversion efficiency of 1.8%∕W.
Optical capacitance-voltage characterization of charge traps in the trapping nitride layer of charge trapped flash memory devices
Authors: Lee Jang Uk. , Roh Kang Seob , Kang Gu Cheol , Seo Seung Hwan , Kim Kwan Young , Lee Sunyeong , Song Kwan Jae , Choi Chang Min , Park So Ra , Park Jun Hyun , Jeon Ki Chan , Kim Dae Hwan , Park Byung-Gook , Lee Jong Duk , Kim Dong Myong
Published: November 2007

Extracting the trap distribution in charge trapping layers of charge trap flash memory devices, an optical C-V method (OCVM) is proposed. Applying photons with λ=532nm to the oxide-nitride-oxide layer with 50∕60∕23Å in metal-oxide-nitride-oxide-semiconductor charge trap flash devices, the trap density in the charge trapping nitride layer is extracted to be 1.16×1018–1.67×1019cm−3eV−1 over the energy EC−Et=1.36–1.64eV. Combining sub-band-gap photons in C-V characterization, the OCVM method is free from the thermal and electrical stresses which are inherent in conventional characterization methods even though they are critical error factors for accurate characterization of charge trapped flash memory devices.
Low noise NbN hot electron bolometer mixer at 4.3THz
Authors: Khosropanah P. , Gao J. R. , Laauwen W. M. , Hajenius M. , Klapwijk T. M.
Published: November 2007

We have studied the sensitivity of a superconducting NbN hot electron bolometer mixer integrated with a spiral antenna at 4.3THz. Using hot/cold blackbody loads and a beam splitter all in vacuum, we measured a double sideband receiver noise temperature of 1300K at the optimum local oscillator (LO) power of 330nW, which is about 12 times the quantum noise (hν∕2kB). Our result indicates that there is no sign of degradation of the mixing process at the superterahertz frequencies. Moreover, a measurement method is introduced which allows us for an accurate determination of the sensitivity despite LO power fluctuations.
Modifications of the exciton lifetime and internal quantum efficiency for organic light-emitting devices with a weak/strong microcavity
Authors: Chen Xue-Wen , Choy Wallace C. H. , Liang C. J. , Wai P. K. A. , He Sailing
Published: November 2007

A comprehensive analysis is given on the modifications of the exciton lifetime and internal quantum efficiency (ηint) for organic light-emitting devices (OLEDs). A linear relation is derived between the exciton lifetime and ηint, which is difficult to measure directly. The internal quantum efficiency can thus be estimated easily through the measurement of the exciton lifetime. The exciton lifetimes for OLEDs with weak or strong microcavity are studied experimentally and theoretically. The modification of the exciton lifetime is well explained through the microcavity effect and surface plasmon resonance. An excellent agreement between the experimental and theoretical results is achieved.
JARID1B is a histone H3 lysine 4 demethylase up-regulated in prostate cancer
Authors: Xiang Yang , Zhu Ziqi , Han Gang , Ye Xiaolei , Xu Bo , Peng Zhouchun , Ma Yuanjun , Yu Yi , Lin Hanqing , Chen Adele Pin , Chen Charlie Degui
Published: November 2007

Histone methylation is a dynamic process that participates in a diverse array of cellular processes and has been found to associate with cancer. Recently, several histone demethylases have been identified that catalyze the removal of methylation from histone H3 lysine residues. Through bioinformatic and biochemical analysis, we identified JARID1B as a H3K4 demethylase. Overexpression of JARID1B resulted in loss of tri-, di-, and monomethyl H3K4 but did not affect other histone lysine methylations.
In vitro
biochemical experiments demonstrated that JARID1B directly catalyzes the demethylation. The enzymatic activity requires the JmjC domain and uses Fe(II) and α-ketoglutarate as cofactors. Furthermore, we found that JARID1B is up-regulated in prostate cancer tissues, compared with benign prostate samples. We also demonstrated that JARID1B associates with androgen receptor and regulates its transcriptional activity. Thus, we identified JARID1B as a demethylase capable of removing three methyl groups from histone H3 lysine 4 and up-regulated in prostate cancer.
Dynamic interplay between nitration and phosphorylation of tubulin cofactor B in the control of microtubule dynamics
Authors: Rayala Suresh K. , Martin Emil , Sharina Iraida G. , Molli Poonam R. , Wang Xiaoping , Jacobson Raymond , Murad Ferid , Kumar Rakesh
Published: November 2007

Tubulin cofactor B (TCoB) plays an important role in microtubule dynamics by facilitating the dimerization of α- and β-tubulin. Recent evidence suggests that p21-activated kinase 1 (Pak1), a major signaling nodule in eukaryotic cells, phosphorylates TCoB on Ser-65 and Ser-128 and plays an essential role in microtubule regrowth. However, to date, no upstream signaling molecules have been identified to antagonize the functions of TCoB, which might help in maintaining the equilibrium of microtubules. Here, we discovered that TCoB is efficiently nitrated, mainly on Tyr-64 and Tyr-98, and nitrated-TCoB attenuates the synthesis of new microtubules. In addition, we found that nitration of TCoB antagonizes signaling-dependent phosphorylation of TCoB, whereas optimal nitration of TCoB requires the presence of functional Pak1 phosphorylation sites, thus providing a feedback mechanism to regulate phosphorylation-dependent MT regrowth. Together these findings identified TCoB as the third cytoskeleton protein to be nitrated and suggest a previously undescribed mechanism, whereby growth factor signaling may coordinately integrate nitric oxide signaling in the regulation of microtubule dynamics.
Redundant and unique roles of retinol dehydrogenases in the mouse retina
Authors: Maeda Akiko , Maeda Tadao , Sun Wenyu , Zhang Houbin , Baehr Wolfgang , Palczewski Krzysztof
Published: November 2007

Highly abundant short-chain alcohol dehydrogenases (RDHs) in the retina were assumed to be involved in the recycling of 11-
cis
-retinal chromophore in the visual cycle. Mutations in human RDH genes are associated with
Fundus albipunctatus
, a mild form of night blindness (
RDH5
) and an autosomal recessive, childhood-onset severe retinal dystrophy (
RDH12
).
Rdh12
knockout mice were found to be susceptible to light-induced photoreceptor apoptosis, whereas
Rdh5
and
Rdh8
knockout mice displayed only delayed dark adaptation. However, each knockout mouse eventually regenerated normal levels of visual pigments, suggesting that RDHs compensate for each other in the visual cycle. Here, we established RDH double knockout (
Rdh8
−/−
Rdh12
−/−
) and triple knockout (
Rdh5
−/−
Rdh8
−/−
Rdh12
−/−
) mice generated on various genetic backgrounds including a rod α-transducin knockout to test cone function. RDH activity was severely reduced in
Rdh8
−/−
Rdh12
−/−
retina extracts, whereas
Rdh8
−/−
RDH activity was intermediate and
Rdh12
−/−
RDH activity was reduced only slightly. Surprisingly, all multiple knockout mice produced sufficient amounts of the chromophore to regenerate rhodopsin and cone pigments
in vivo
. Three-month-old
Rdh8
−/−
Rdh12
−/−
mice characteristically displayed a slowly progressing rod–cone dystrophy accompanied by accumulation of
N
-retinylidene-
N
-retinylethanolamine (A2E), a toxic substance known to contribute to retinal degeneration. A2E accumulation and retinal degeneration were prevented by application of retinylamine, a potent retinoid cycle inhibitor. The results suggest that RDH8 and RDH12 are dispensable in support of the visual cycle but appear to be key components in clearance of free all-
trans
-retinal, thereby preventing A2E accumulation and photoreceptor cell death.
Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms
Authors: Moore Michael J. , Bell Charles D. , Soltis Pamela S. , Soltis Douglas E.
Published: November 2007

Although great progress has been made in clarifying deep-level angiosperm relationships, several early nodes in the angiosperm branch of the Tree of Life have proved difficult to resolve. Perhaps the last great question remaining in basal angiosperm phylogeny involves the branching order among the five major clades of mesangiosperms (Ceratophyllum, Chloranthaceae, eudicots, magnoliids, and monocots). Previous analyses have found no consistent support for relationships among these clades. In an effort to resolve these relationships, we performed phylogenetic analyses of 61 plastid genes (≈42,000 bp) for 45 taxa, including members of all major basal angiosperm lineages. We also report the complete plastid genome sequence ofCeratophyllum demersum. Parsimony analyses of combined and partitioned data sets varied in the placement of several taxa, particularlyCeratophyllum, whereas maximum-likelihood (ML) trees were more topologically stable. Total evidence ML analyses recovered a clade of Chloranthaceae + magnoliids as sister to a well supported clade of monocots + (Ceratophyllum+ eudicots). ML bootstrap and Bayesian support values for these relationships were generally high, although approximately unbiased topology tests could not reject several alternative topologies. The extremely short branches separating these five lineages imply a rapid diversification estimated to have occurred between 143.8 ± 4.8 and 140.3 ± 4.8 Mya.
A helix-breaking mutation in TRPML3 leads to constitutive activity underlying deafness in the varitint-waddler mouse
Authors: Grimm Christian , Cuajungco Math P. , van Aken Alexander F. J. , Schnee Michael , Jörs Simone , Kros Corné J. , Ricci Anthony J. , Heller Stefan
Published: November 2007

Homozygote varitint-waddler (
Va
) mice, expressing a mutant isoform (A419P) of TRPML3 (mucolipin 3), are profoundly deaf and display vestibular and pigmentation deficiencies, sterility, and perinatal lethality. Here we show that the varitint-waddler isoform of TRPML3 carrying an A419P mutation represents a constitutively active cation channel that can also be identified in native varitint-waddler hair cells as a distinct inwardly rectifying current. We hypothesize that the constitutive activation of TRPML3 occurs as a result of a helix-breaking proline substitution in transmembrane-spanning domain 5 (TM5). A proline substitution scan demonstrated that the inner third of TRPML3's TM5 is highly susceptible to proline-based kinks. Proline substitutions in TM5 of other TRP channels revealed that TRPML1, TRPML2, TRPV5, and TRPV6 display a similar susceptibility at comparable positions, whereas other TRP channels were not affected. We conclude that the molecular basis for deafness in the varitint-waddler mouse is the result of hair cell death caused by constitutive TRPML3 activity. To our knowledge, our study provides the first direct mechanistic link of a mutation in a TRP ion channel with mammalian hearing loss.
Paxillin Phosphorylation Controls Invadopodia/Podosomes Spatiotemporal Organization
Authors: Badowski Cédric , Pawlak Géraldine , Grichine Alexei , Chabadel Anne , Oddou Christiane , Jurdic Pierre , Pfaff Martin , Albigès-Rizo Corinne , Block Marc R.
Published: November 2007

In Rous sarcoma virus (RSV)-transformed baby hamster kidney (BHK) cells, invadopodia can self-organize into rings and belts, similarly to podosome distribution during osteoclast differentiation. The composition of individual invadopodia is spatiotemporally regulated and depends on invadopodia localization along the ring section: the actin core assembly precedes the recruitment of surrounding integrins and integrin-linked proteins, whereas the loss of the actin core was a prerequisite to invadopodia disassembly. We have shown that invadopodia ring expansion is controlled by paxillin phosphorylations on tyrosine 31 and 118, which allows invadopodia disassembly. In BHK-RSV cells, ectopic expression of the paxillin mutant Y31F-Y118F induces a delay in invadopodia disassembly and impairs their self-organization. A similar mechanism is unraveled in osteoclasts by using paxillin knockdown. Lack of paxillin phosphorylation, calpain or extracellular signal-regulated kinase inhibition, resulted in similar phenotype, suggesting that these proteins belong to the same regulatory pathways. Indeed, we have shown that paxillin phosphorylation promotes Erk activation that in turn activates calpain. Finally, we observed that invadopodia/podosomes ring expansion is required for efficient extracellular matrix degradation both in BHK-RSV cells and primary osteoclasts, and for transmigration through a cell monolayer.
Conversion of a Replication Origin to a Silencer through a Pathway Shared by a Forkhead Transcription Factor and an S Phase Cyclin
Authors: Casey Laurieann , Patterson Erin E. , Müller Ulrika , Fox Catherine A.
Published: November 2007

Silencing of the mating-type locus HMR in Saccharomyces cerevisiae requires DNA elements called silencers. To establish HMR silencing, the origin recognition complex binds the HMR-E silencer and recruits the silent information regulator (Sir)1 protein. Sir1 in turn helps establish silencing by stabilizing binding of the other Sir proteins, Sir2–4. However, silencing is semistable even in sir1Δ cells, indicating that SIR1-independent establishment mechanisms exist. Furthermore, the requirement for SIR1 in silencing a sensitized version of HMR can be bypassed by high-copy expression of FKH1 (FKH1hc), a conserved forkhead transcription factor, or by deletion of the S phase cyclin CLB5 (clb5Δ). FKH1hccaused only a modest increase in Fkh1 levels but effectively reestablished Sir2–4 chromatin at HMR as determined by Sir3-directed chromatin immunoprecipitation. In addition, FKH1hcprolonged the cell cycle in a manner distinct from deletion of its close paralogue FKH2, and it created a cell cycle phenotype more reminiscent to that caused by a clb5Δ. Unexpectedly, and in contrast to SIR1, both FKH1hcand clb5Δ established silencing at HMR using the replication origins, ARS1 or ARSH4, as complete substitutes for HMR-E (HMRΔE::ARS). HMRΔE::ARS1 was a robust origin in CLB5 cells. However, initiation by HMRΔE::ARS1 was reduced by clb5Δ or FKH1hc, whereas ARS1 at its native locus was unaffected. The CLB5-sensitivity of HMRΔE::ARS1 did not result from formation of Sir2–4 chromatin because sir2Δ did not rescue origin firing in clb5Δ cells. These and other data supported a model in which FKH1 and CLB5 modulated Sir2–4 chromatin and late-origin firing through opposing regulation of a common pathway.
Sequestration of Mutated α1-Antitrypsin into Inclusion Bodies Is a Cell-protective Mechanism to Maintain Endoplasmic Reticulum Function
Authors: Granell Susana , Baldini Giovanna , Mohammad Sameer , Nicolin Vanessa , Narducci Paola , Storrie Brian , Baldini Giulia
Published: November 2007

A variant α1-antitrypsin with E342K mutation has a high tendency to form intracellular polymers, and it is associated with liver disease. In the hepatocytes of individuals carrying the mutation, α1-antitrypsin localizes both to the endoplasmic reticulum (ER) and to membrane-surrounded inclusion bodies (IBs). It is unclear whether the IBs contribute to cell toxicity or whether they are protective to the cell. We found that in hepatoma cells, mutated α1-antitrypsin exited the ER and accumulated in IBs that were negative for autophagosomal and lysosomal markers, and contained several ER components, but not calnexin. Mutated α1-antitrypsin induced IBs also in neuroendocrine cells, showing that formation of these organelles is not cell type specific. In the presence of IBs, ER function was largely maintained. Increased levels of calnexin, but not of protein disulfide isomerase, inhibited formation of IBs and lead to retention of mutated α1-antitrypsin in the ER. In hepatoma cells, shift of mutated α1-antitrypsin localization to the ER by calnexin overexpression lead to cell shrinkage, ER stress, and impairment of the secretory pathway at the ER level. We conclude that segregation of mutated α1-antitrypsin from the ER to the IBs is a protective cell response to maintain a functional secretory pathway.
The 90-kDa Heat Shock Protein Stabilizes the Polysomal Ribonuclease 1 mRNA Endonuclease to Degradation by the 26S Proteasome
Authors: Peng Yong , Liu Xiaoqiang , Schoenberg Daniel R.
Published: November 2007

The polysomal ribonuclease 1 (PMR1) mRNA endonuclease forms a selective complex with its translating substrate mRNAs where it is activated to initiate mRNA decay. Previous work showed tyrosine phosphorylation is required for PMR1 targeting to this polysome-bound complex, and it identified c-Src as the responsible kinase. c-Src phosphorylation occurs in a distinct complex, and the current study shows that 90-kDa heat shock protein (Hsp90) is also recovered with PMR1 and c-Src. Hsp90 binding to PMR1 is inhibited by geldanamycin, and geldanamycin stabilizes substrate mRNA to PMR1-mediated decay. PMR1 is inherently unstable and geldanamycin causes PMR1 to rapidly disappear in a process that is catalyzed by the 26S proteasome. We present a model where Hsp90 interacts transiently to stabilize PMR1 in a manner similar to its interaction with c-Src, thus facilitating the tyrosine phosphorylation and targeting of PMR1 to polysomes.
The Golgi Protein GM130 Regulates Centrosome Morphology and Function
Authors: Kodani Andrew , Sütterlin Christine
Published: November 2007

The Golgi apparatus (GA) of mammalian cells is positioned in the vicinity of the centrosome, the major microtubule organizing center of the cell. The significance of this physical proximity for organelle function and cell cycle progression is only beginning to being understood. We have identified a novel function for the GA protein, GM130, in the regulation of centrosome morphology, position and function during interphase. RNA interference–mediated depletion of GM130 from five human cell lines revealed abnormal interphase centrosomes that were mispositioned and defective with respect to microtubule organization and cell migration. When GM130-depleted cells entered mitosis, they formed multipolar spindles, arrested in metaphase, and died. We also detected aberrant centrosomes during interphase and multipolar spindles during mitosis in ldlG cells, which do not contain detectable GM130. Although GA proteins have been described to regulate mitotic centrosomes and spindle formation, this is the first report of a role for a GA protein in the regulation of centrosomes during interphase.
Methermicoccus shengliensis gen. nov., sp. nov., a thermophilic, methylotrophic methanogen isolated from oil-production water, and proposal of Methermicoccaceae fam. nov.
Authors: Cheng Lei , Qiu Tian-Lei , Yin Xiao-Bo , Wu Xiao-Lei , Hu Guo-Quan , Deng Yu , Zhang Hui
Published: November 2007

A thermophilic, methylotrophic methanogen, strain ZC-1T, was isolated from the Shengli oilfield, China. Cells of strain ZC-1Twere motile cocci, 0.7–1.0 μm in diameter and always occurred in clusters of two to four cells. Lysis-susceptibility experiments and analysis of transmission electron micrographs of strain ZC-1Tsuggested the presence of a proteinaceous cell wall. Strain ZC-1Tused methanol, methylamine and trimethylamine as substrates for methanogenesis. Optimal growth, with a doubling time of around 5 h, occurred at pH 6.0–6.5, 65 °C, 0.3–0.5 M NaCl and 0.05–0.20 M MgCl2. The DNA G+C content of this organism was 56 mol%. Analysis of 16S rRNA gene sequence and the inferred amino acid sequence of themcrAgene of strain ZC-1Tindicated that it is related specifically to members of the familyMethanosaetaceae(90.6 and 76.6 % sequence similarity, respectively). However, strain ZC-1Tfailed to grow with acetate as substrate for methanogenesis, which is a special characteristic of the familyMethanosaetaceae. Based on these phenotypic and phylogenic characteristics, strain ZC-1Tis proposed to represent a novel genus and species, for which the nameMethermicoccus shengliensisgen. nov., sp. nov. is proposed. The type strain is ZC-1T(=CGMCC 1.5056T=DSM 18856T).Methermicoccaceaefam. nov. is also proposed.
Nocardia speluncae sp. nov., isolated from a cave
Authors: Seo Jae Pyo , Yun Yoe-Won , Lee Soon Dong
Published: November 2007

The taxonomic status of a mycolic acid-containing actinomycete, isolated from a natural cave on Jeju Island, Republic of Korea, was investigated by means of a polyphasic approach. The isolate, designated strain N2-11T, produced yellow- to orange-coloured vegetative hyphae and white- to pinkish white-coloured aerial mycelia, both of which fragmented into irregular rod-shaped elements. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the organism belonged to the family Nocardiaceae, occupying a distinct position between Nocardia harenae and a Nocardia carnea cluster. The results of chemotaxonomic analyses were consistent with the affiliation of the organism with the genus Nocardia. On the basis of 16S rRNA gene sequence similarities, the closest phylogenetic neighbours were the type strains of N. carnea (98.3 %), Nocardia flavorosea (98.0 %), Nocardia sienata (97.9 %) and Nocardia testacea (97.8 %), but the organism could be clearly distinguished from its phylogenetic relatives with reference to a broad range of physiological markers. On the basis of phenotypic and molecular genetic data presented in this study, strain N2-11T represents a novel species of the genus Nocardia, for which the name Nocardia speluncae sp. nov. is proposed. The type strain is N2-11T (=JBRI 2006T =KCTC 19223T =DSM 45078T).
Nocardioides marinisabuli sp. nov., a novel actinobacterium isolated from beach sand
Authors: Lee Dong Wan , Hyun Chang-Gu , Lee Soon Dong
Published: November 2007

The taxonomic position of a novel actinobacterium (designated SBS-12T), which was isolated from beach sand on Jeju Island, Republic of Korea, was determined following a polyphasic taxonomic characterization. Cells of the organism were Gram-positive, catalase-positive, oxidase-negative and non-motile rods. The organism contained ll-diaminopimelic acid in the cell-wall peptidoglycan and MK-8(H4) as predominant menaquinone, and had a polar lipid profile containing phosphatidylglycerol and phosphatidylinositol, iso-C16 : 0 as the major fatty acid and a DNA G+C content of 73.1 mol%. A neighbour-joining tree based on 16S rRNA gene sequences showed that the organism occupies a distinct phylogenetic position within the radiation including representatives of the family Nocardioidaceae. High levels of 16S rRNA gene sequence similarity were found with Nocardioides kribbensis (97.2 %), Nocardioides aquiterrae (96.9 %), Nocardioides pyridinolyticus (96.6 %) and Nocardioides aquaticus (96.3 %). The combination of morphological and chemotaxonomic characteristics was consistent with classification in the genus Nocardioides, but the isolate can be differentiated from all Nocardioides species with validly published names by a range of physiological properties. The name Nocardioides marinisabuli sp. nov. is proposed for this novel organism, with the type strain SBS-12T (=JBRI 2003T=KCCM 42681T=DSM 18965T).
Azospirillum zeae sp. nov., a diazotrophic bacterium isolated from rhizosphere soil of Zea mays
Authors: Mehnaz Samina , Weselowski Brian , Lazarovits George
Published: November 2007

Two free-living nitrogen-fixing bacterial strains, N6 and N7T, were isolated from corn rhizosphere. A polyphasic taxonomic approach, including morphological characterization, Biolog analysis, DNA–DNA hybridization, and 16S rRNA, cpn60 and nifH gene sequence analysis, was taken to analyse the two strains. 16S rRNA gene sequence analysis indicated that strains N6 and N7T both belonged to the genus Azospirillum and were closely related to Azospirillum oryzae (98.7 and 98.8 % similarity, respectively) and Azospirillum lipoferum (97.5 and 97.6 % similarity, respectively). DNA–DNA hybridization of strains N6 and N7T showed reassociation values of 48 and 37 %, respectively, with A. oryzae and 43 % with A. lipoferum. Sequences of the nifH and cpn60 genes of both strains showed 99 and ~95 % similarity, respectively, with those of A. oryzae. Chemotaxonomic characteristics (Q-10 as quinone system, 18 : 1ω7c as major fatty acid) and G+C content of the DNA (67.6 mol%) were also similar to those of members of the genus Azospirillum. Gene sequences and Biolog and fatty acid analysis showed that strains N6 and N7T differed from the closely related species A. lipoferum and A. oryzae. On the basis of these results, it is proposed that these nitrogen-fixing strains represent a novel species. The name Azospirillum zeae sp. nov. is suggested, with N7T (=NCCB 100147T=LMG 23989T) as the type strain.
Bacillus kribbensis sp. nov., isolated from a soil sample in Jeju, Korea
Authors: Lim Jee-Min , Jeon Che Ok , Lee Jung Ro , Park Dong-Jin , Kim Chang-Jin
Published: November 2007

A Gram-positive, endospore-forming bacterium, designated strain BT080T, was isolated from a soil sample in Jeju, Korea. Cells of the isolate were strictly aerobic rods that were motile by means of peritrichous flagella. The strain grew optimally at 30–33 °C and pH 5.5–6.5. Chemotaxonomic data (major isoprenoid quinone, MK-7; DNA G+C content, 43.3 mol%; major fatty acids, anteiso-C15 : 0, iso-C14 : 0, iso-C16 : 0 and iso-C15 : 0) supported the affiliation of the isolate to the genus Bacillus. Comparative 16S rRNA gene sequence analyses showed that strain BT080T formed a distinct phyletic line within the genus Bacillus. The levels of 16S rRNA gene sequence similarity with respect to related Bacillus species were below 96.4 %. On the basis of physiological, biochemical and phylogenetic properties, strain BT080T represents a novel species within the genus Bacillus, for which the name Bacillus kribbensis sp. nov. is proposed. The type strain is BT080T (=KCTC 13934T=DSM 17871T).
Salegentibacter salarius sp. nov., isolated from a marine solar saltern
Authors: Yoon Jung-Hoon , Jung Seo-Youn , Kang So-Jung , Jung Yong-Taek , Oh Tae-Kwang
Published: November 2007

A Gram-negative, non-motile, rod-shaped bacterium, strain ISL-6T, phenotypically resembling members of the genus Salegentibacter, was isolated from a marine solar saltern of the Yellow Sea in Korea and subjected to a polyphasic taxonomic investigation. Strain ISL-6T grew optimally at pH 7.0–8.0 and 30 °C and in the presence of 8 % (w/v) NaCl. It contained MK-6 as the predominant menaquinone. The major fatty acids were iso-C15 : 0 and anteiso-C15 : 0. The DNA G+C content was 37.5 mol%. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain ISL-6T belonged to the genus Salegentibacter. Strain ISL-6T exhibited 16S rRNA gene sequence similarity values of 92.0–98.6 % with respect to the type strains of recognized Salegentibacter species. Low DNA–DNA relatedness values, differential phenotypic properties and phylogenetic distinctiveness demonstrated that strain ISL-6T is distinguishable from the recognized Salegentibacter species. Therefore strain ISL-6T represents a novel species of the genus Salegentibacter, for which the name Salegentibacter salarius sp. nov. is proposed. The type strain is ISL-6T (=KCTC 12974T =CCUG 54355T).
Lewinella agarilytica sp. nov., a novel marine bacterium of the phylum Bacteroidetes, isolated from beach sediment
Authors: Lee Soon Dong
Published: November 2007

A Gram-negative, aerobic, light-orange-coloured, marine bacterium (designated SST-19T) was isolated from beach sediment in Jeju, Korea, and its taxonomic position was determined by means of a polyphasic approach. In a neighbour-joining phylogenetic tree based on 16S rRNA gene sequences, strain SST-19T was positioned within the family ‘Saprospiraceae’, class Sphingobacteria, and formed a consistent cluster with Lewinella persica ATCC 23167T (94.7 % sequence similarity). The levels of 16S rRNA gene sequence similarity between the isolate and recognized members of the family ranged from 84 to 89 %, with Lewinella cohaerens ATCC 23123T, Lewinella nigricans ATCC 23147T, Haliscomenobacter hydrossis DSM 1100T and Saprospira grandis ATCC 23119T showing values of 89.0 , 88.4 , 86.4 and 84.1 %, respectively. Strain SST-19T required seawater for growth and its cells were unbranched, flexible rods or filaments with gliding motility. The cellular fatty acids consisted mainly of saturated, unsaturated and iso-branched fatty acids, the major components being C16 : 1
ω7c and/or iso-C15 : 0 2-OH (24.1 %), C18 : 0 (13.5 %), iso-C15 : 0 (11.1 %) and C16 : 0 (10.9 %). The G+C content of the DNA was found to be 51.3 mol%. On the basis of the results from phenotypic and phylogenetic analyses, the isolate represents a novel species of the genus Lewinella, for which the name Lewinella agarilytica sp. nov. is proposed. The type strain is SST-19T (=JBRI 2009T=KCTC 12774T=JCM 14216T).
Ulvibacter antarcticus sp. nov., isolated from Antarctic coastal seawater
Authors: Choi Tae-Hwan , Lee Hong Kum , Lee Kiyoung , Cho Jang-Cheon
Published: November 2007

A seawater bacterium, designated IMCC3101T, was isolated from Antarctic coastal seawater. The strain was Gram-negative, chemoheterotrophic, obligately aerobic, pigmented dark yellow (flexirubin-type pigments) and devoid of gliding and flagellar motility. On the basis of 16S rRNA gene sequence comparisons, the most closely related species was Ulvibacter litoralis (96.6 %). Phylogenetic trees generated by using 16S rRNA gene sequences confirmed that the strain belonged to the genus Ulvibacter in the family Flavobacteriaceae. The DNA G+C content was 37.0 mol% and the major respiratory quinone was MK-6. Several phenotypic characteristics, including cell and colony morphology, the absence of gliding motility and the temperature range for growth, serve to differentiate the strain from the only species in the genus Ulvibacter with a validly published name (U. litoralis). Therefore, strain IMCC3101T represents a novel species of the genus Ulvibacter, for which the name Ulvibacter antarcticus sp. nov. is proposed. The type strain is IMCC3101T (=KCCM 42686T=NBRC 102682T).
Sejongia marina sp. nov., isolated from Antarctic seawater
Authors: Lee Kiyoung , Lee Hong Kum , Choi Tae-Hwan , Cho Jang-Cheon
Published: November 2007

A Gram-negative, psychrotolerant, chemoheterotrophic, aerobic, non-gliding, non-motile, yellow-pigmented bacterium, designated IMCC3228T, was isolated from coastal seawater of the Antarctic. On the basis of 16S rRNA gene sequence comparisons, the strain was most closely related to the genera Sejongia (95.3–96.1 %) and Chryseobacterium (94.2–95.9 %) in the family Flavobacteriaceae. Phylogenetic trees generated using several treeing algorithms based on 16S rRNA gene sequences showed that this Antarctic marine isolate formed a distinct phyletic line within the genus Sejongia. The DNA G+C content of the strain was 35.0 mol% and the major respiratory quinone was MK-6. Several phenotypic and chemotaxonomic characteristics, including temperature and NaCl optima for growth, oxidase activity and the proportions of major cellular fatty acids, served to differentiate the strain from the recognized species of the genus Sejongia. Therefore strain IMCC3228T represents a novel species of the genus Sejongia, for which the name Sejongia marina sp. nov. is proposed. The type strain is IMCC3228T (=KCCM 42689T=NBRC 103143T).
Knoellia aerolata sp. nov., isolated from an air sample in Korea
Authors: Weon Hang-Yeon , Kim Byung-Yong , Schumann Peter , Kroppenstedt Reiner M. , Noh Hyung-Jun , Park Chan-Won , Kwon Soon-Wo
Published: November 2007

An aerobic, Gram-positive, non-motile, non-spore-forming, rod–coccus-shaped bacterium, strain 5317S-21T, was isolated from an air sample from Suwon city, Republic of Korea. The isolate was able to grow within a pH range of 5.0–9.0 and a temperature range of 5–35 °C and it tolerated up to 2 % (w/v) NaCl. The cell-wall peptidoglycan contained meso-diaminopimelic acid as diagnostic diamino acid. The predominant isoprenoid quinone was MK-8(H4). The major polar lipids were phosphatidylinositol, phosphatidylethanolamine and diphosphatidylglycerol; phosphatidylglycerol and several unknown phospholipids were also detected. Mycolic acids were absent. The only whole-cell sugar was glucose. The major cellular fatty acids were iso-C16 : 0, C17 : 1
ω8c and iso-C15 : 0. 16S rRNA gene sequence analysis indicated that strain 5317S-21T was related phylogenetically to members of the genus Knoellia, with 97.4 % sequence similarity to the type strains of Knoellia sinensis and Knoellia subterranea. The G+C content of the genomic DNA of strain 5317S-21T was 73 mol%. Levels of DNA–DNA relatedness between strain 5317S-21T and the type strains of Knoellia sinensis and Knoellia subterranea were 37 and 41 %, respectively. It was concluded that strain 5317S-21T represents a novel species of the genus Knoellia, for which the name Knoellia aerolata sp. nov. is proposed. The type strain is 5317S-21T (=KACC 20583T =DSM 18566T).
Leading terms of Artin L-functions at s=0 and s=1
Authors: Breuning Manuel , Burns David
Published: November 2007

We formulate an explicit conjecture for the leading term at s=1 of the equivariant Dedekind zeta-function that is associated to a Galois extension of number fields. We show that this conjecture refines well-known conjectures of Stark and Chinburg, and we use the functional equation of the zeta-function to compare it to a natural conjecture for the leading term at s=0.
Determining Fitting ideals of minus class groups via the equivariant Tamagawa number conjecture
Authors: Greither Cornelius
Published: November 2007

We assume the validity of the equivariant Tamagawa number conjecture for a certain motive attached to an abelian extension K/k of number fields, and we calculate the Fitting ideal of the dual of clK− as a Galois module, under mild extra hypotheses on K/k. This builds on concepts and results of Tate, Burns, Ritter and Weiss. If k is the field of rational numbers, our results are unconditional.
Counterexamples to Okounkov’s log-concavity conjecture
Authors: Chindris Calin , Derksen Harm , Weyman Jerzy
Published: November 2007

We give counterexamples to Okounkov’s log-concavity conjecture for Littlewood–Richardson coefficients.
Variation de la dimension relative en géométrie analytique p-adique
Authors: Ducros Antoine
Published: November 2007

Let k be a complete, non-Archimedean valued field (the trivial absolute value is allowed) and let φ:X→Y be a morphism between two Berkovich k-analytic spaces; we show that, for any integer n, the set of points of X at which the local dimension of φ is at least equal to n is a Zariski-closed subset of X. In order to establish it, we first prove an analytic analogue of Zariski’s Main Theorem, and we also introduce, and study, the notion of an analytic system of parameters at a point.
Flank Modification Methodology for Face-Hobbing Hypoid Gears Based on Ease-Off Topography
Authors: Shih Yi-Pei , Fong Zhang-Hua
Published: November 2007

The fundamental design of spiral bevel and hypoid gears is usually based on a local synthesis and a tooth contact analysis of the gear drive. Recently, however, several flank modification methodologies have been developed to reduce running noise and avoid edge contact in gear making, including modulation of tooth surfaces under predesigned transmission errors. This paper proposes such a flank modification methodology for face-hobbing spiral bevel and hypoid gears based on the ease-off topography of the gear drive. First, the established mathematical model of a universal face-hobbing hypoid gear generator is applied to investigate the ease-off deviations of the design parameters—including cutter parameters, machine settings, and the polynomial coefficients of the auxiliary flank modification motion. Subsequently, linear regression is used to modify the tooth flanks of a gear pair to approximate the optimum ease-off topography suggested by experience. The proposed method is then illustrated using a numerical example of a face-hobbing hypoid gear pair from Oerlikon’s Spiroflex cutting system. This proposed flank modification methodology can be used as a basis for developing a general technique of flank modification for similar types of gears.
Cartesian Parallel Manipulators With Pseudoplanar Limbs
Authors: Lee Chung-Ching , Hervé Jacques M.
Published: November 2007

Based on the Lie-group-algebraic properties of the displacement set, the three-degree-of-freedom (3DOF) pseudoplanar motion often termed Y motion for brevity is first introduced. Then, all possible general architectures of the mechanical generators of a given Y subgroup are obtained by implementing serial arrays of 1DOF Reuleaux pairs or hinged parallelograms. In total, five distinct mechanical generators of Y motion are revealed and seven ones having at least one parallelogram are also derived from them. In order to avoid the singularity that may occur in the limbs, all singular postures of Y-motion generators are also located by detecting the possible linear dependency of the joint twists and the group dependency of displacement sets. The parallel layout of three 4DOF limbs including Y-motion generators with orthogonal planes make up a Cartesian translational parallel manipulator, which produces a motion set of spatial translations. The 3DOF translation of the moving platform is directly controlled by the three 1DOF translations in three orthogonal prismatic fixed joints.
Study on the High-Sealing of Roots Rotor With Variable Trochoid Ratio
Authors: Hsieh Chiu-Fan , Hwang Yii-Wen
Published: November 2007

Vacuum pump plays an important role in the vacuum system. In this paper, a new method is proposed to design the Roots rotor that was the trochoidal curve with variable trochoid ratio. The fifth-order polynomial and cubic spline functions are used to generate smoothly trochoid ratio functions and thus a regular addendum curve for Roots rotor will be generated. Based on the addendum curve, the tooth profile for the complete Roots rotor is derived by the gearing theory. In order to improve the sealing between the rotor tip and the chamber, a design procedure is also developed for roots rotor with high sealing and high area efficiency. In addition, the undercutting equation is used to study the constraints of design parameters and the center of curvature is used to check the occurrence of the carryover on the tooth profile. Finally, some design examples are presented to show the feasibility of the proposed method.
Integration of User Perceptions in the Design Process: Application to Musical Instrument Optimization
Authors: Poirson Emilie , Petiot Jean-François , Gilbert Joël
Published: November 2007

This paper describes a user-centered design method, which allows the integration of user’s perceptions in different stages of the design process, by taking into account his/her needs and preferences. It relies on two domains which remain generally distinct: the design with a scientific approach (generally math based) and the integration of users’ perceptions, preferences, tastes, inherently subjective. We apply this method to the design of musical instruments, products for which the feelings of the user are of prime importance, and remain so far difficult to integrate for the design/improvement of an instrument. The methodology is made of two main stages: (1) a subjective study, based on the sensory analysis techniques, during which a “product space” (a family of trumpets) is assessed by a panel of experts according to sensory attributes, and (2) an objective study of the instruments, based on the physical measurement of a specific characteristic of brasses: the acoustic input impedance. Then, data analysis is used to correlate perceptive and objective evaluations, in order to deduce design rules and to formulate the improvement of a perceptive characteristic of the product (the intonation) as a multicriteria optimization problem. The design of the inner shape (the bore) of a “new” instrument is finally made by solving the multicriteria optimization problem using genetic algorithms.
Low Volume Plastics Manufacturing Strategies
Authors: Karania Ruchi , Kazmer David
Published: November 2007

Plastic components are vital components of many engineered products, frequently representing 20–40% of the product value. While injection molding is the most common process for economically producing complex designs in large quantities, a large initial monetary investment and extended development time are required to develop appropriate tooling. For applications with lower or unknown production quantities, designers may prefer another process that has a lower development cost and lead time albeit with higher marginal costs and production times. A methodology is presented that assists the designer to select the most appropriate manufacturing process that trades off the total production costs with production lead times. The approach is to develop aggregate component cost and lead-time models as a function of production quantity from extensive industry data for an electrical enclosure consisting of two components. Binding quotes were secured from multiple suppliers for a variety of manufacturing processes including computer numerical control machining, fused deposition modeling, selective laser sintering, vacuum casting, direct fabrication, and injection molding with soft prototype and production tooling. The methodology yields a Pareto optimal set that compares the production costs and lead times as a function of the production quantity. The results indicate that the average cost per enclosure assembly is highly sensitive to the production quantity, with average costs varying by more than a factor of 100 for production quantities varying between 100 and 10,000 assemblies. Each of the processes is competitive with respect to total production cost and total production lead time under differing conditions; a flow chart is provided as an example of a decision support tool that can be provided to assist process selection during the product development process and thereby reduce the product development time and cost.
Direct Observation of Chaperone-Induced Changes in a Protein Folding Pathway
Authors: Bechtluft Philipp , van Leeuwen Ruud G. H. , Tyreman Matthew , Tomkiewicz Danuta , Nouwen Nico , Tepper Harald L. , Driessen Arnold J. M. , Tans Sander J.
Published: November 2007

How chaperone interactions affect protein folding pathways is a central problem in biology. With the use of optical tweezers and all-atom molecular dynamics simulations, we studied the effect of chaperone SecB on the folding and unfolding pathways of maltose binding protein (MBP) at the single-molecule level. In the absence of SecB, we find that the MBP polypeptide first collapses into a molten globulelike compacted state and then folds into a stable core structure onto which several α helices are finally wrapped. Interactions with SecB completely prevent stable tertiary contacts in the core structure but have no detectable effect on the folding of the external α helices. It appears that SecB only binds to the extended or molten globulelike structure and retains MBP in this latter state. Thus during MBP translocation, no energy is required to disrupt stable tertiary interactions.
Comment on "Decagonal and Quasi-Crystalline Tilings in Medieval Islamic Architecture"
Authors: Makovicky Emil
Published: November 2007

Lu and Steinhardt (Reports, 23 February 2007, p. 1106) claimed the discovery of a large, potentially quasi-crystalline Islamic tiling in the Darb-i Imam shrine but regard the earlier Maragha tiling, previously described as quasiperiodic, as a small isolated motif. We demonstrate that the Darb-i Imam pattern is periodic and that the quasi-crystalline discs superimposed on its lattice are derivatives of the Maragha pattern.
Carbon Dioxide Activation at the Ni,Fe-Cluster of Anaerobic Carbon Monoxide Dehydrogenase
Authors: Jeoung Jae-Hun , Dobbek Holger
Published: November 2007

Anaerobic CO dehydrogenases catalyze the reversible oxidation of CO to CO
2
at a complex Ni-, Fe-, and S-containing metal center called cluster C. We report crystal structures of CO dehydrogenase II from
Carboxydothermus hydrogenoformans
in three different states. In a reduced state, exogenous CO
2
supplied in solution is bound and reductively activated by cluster C. In the intermediate structure, CO
2
acts as a bridging ligand between Ni and the asymmetrically coordinated Fe, where it completes the square-planar coordination of the Ni ion. It replaces a water/hydroxo ligand bound to the Fe ion in the other two states. The structures define the mechanism of CO oxidation and CO
2
reduction at the Ni-Fe site of cluster C.
Fluctuation Superconductivity in Mesoscopic Aluminum Rings
Authors: Koshnick Nicholas C. , Bluhm Hendrik , Huber Martin E. , Moler Kathryn A.
Published: November 2007

Fluctuations are important near phase transitions, where they can be difficult to describe quantitatively. Superconductivity in mesoscopic rings is particularly intriguing because the critical temperature is an oscillatory function of magnetic field. There is an exact theory for thermal fluctuations in one-dimensional superconducting rings, which are therefore expected to be an excellent model system. We measured the susceptibility of many rings, one ring at a time, by using a scanning superconducting quantum interference device that can isolate magnetic signals that are seven orders of magnitude smaller than applied flux. We find that the fluctuation theory describes the results and that a single parameter characterizes the ways in which the fluctuations are especially important at magnetic fields where the critical temperature is suppressed.
Spontaneous Recovery in Acute Human Hepatitis C Virus Infection: Functional T-Cell Thresholds and Relative Importance of CD4 Help
Authors: Smyk-Pearson Susan , Tester Ian A. , Klarquist Jared , Palmer Brent E. , Pawlotsky Jean-Michel , Golden-Mason Lucy , Rosen Hugo R.
Published: November 2007

The mechanisms mediating protective immunity to hepatitis C virus (HCV) infection are incompletely understood because early infection in humans is rarely identified, particularly in those individuals who subsequently demonstrate spontaneous virus eradication. We have established a large national network of patients with acute HCV infection. Here, we comprehensively examined total HCV-specific CD4
+
and CD8
+
T-cell responses and identified functional T-cell thresholds that predict recovery. Interestingly, we found that the presence of HCV-specific cytotoxic T lymphocytes (CTLs) that can proliferate, exhibit cytotoxicity, and produce gamma interferon does not ensure recovery, but whether these CTLs were primed in the presence or absence of CD4
+
T-cell help (HCV-specific interleukin-2 production) is a critical determinant. These results have important implications for early prediction of the virologic outcome following acute HCV and for the development of novel immunotherapeutic approaches.