bluuebunny/crossref_metadata_2025 huggingface dataset:
Greenland surface melt trends 1973–2007: Evidence of a large increase in 2007
Authors: Mote Thomas L.
Published: November 2007

A time series of surface melt extent, frequency and onset has been updated to include data from Electrically Scanning Microwave Radiometer (ESMR) (1973, 1974 and 1976), Scanning Multichannel Microwave Radiometer (SMMR) (1979–1987) and the Special Sensor Microwave/Imager (SSM/I) (1987–2007). The seasonal melt departure (SMD), the sum from 1 June to 31 August of the departure from average of each day's melt extent, is a new metric used to describe the amount of melt. Results show a large increase in melt in summer 2007, 60% more than the previous high in 1998. During summer 2007, some locations south of 70°N had as many as 50 more days of melt than average. Melt occurred as much as 30 days earlier than average. The SMD is shown to be significantly related to temperatures at coastal meteorological stations, although 2007 had more melt than might be expected based on the summer temperature record.
Three‐dimensional shoaling of large‐amplitude internal waves
Authors: Vlasenko V. , Stashchuk N.
Published: November 2007

The three‐dimensional (3‐D) shoaling of large‐amplitude internal waves (LAIW) is studied in the framework of a fully nonlinear nonhydrostatic numerical model. The vertical fluid stratification, parameters of the propagating waves and bottom topography were taken close to those observed in the northern part of the Andaman Sea. It was found that three‐dimensional evolution of LAIWs propagating from the deep part of a basin onto the shelf differs from two‐dimensional shoaling in many ways largely because of the process of wave refraction developing in the areas of local bottom elevations or depressions. In the 3‐D case the wave refraction produces concave and convex fragments of the wave fronts which may lead to the transverse redistribution of energy along the wave. Results demonstrate that concave wave fragments work as optical lenses focusing the wave energy to the centers of curvature. This process is especially important for LAIWs in shallow water zones where wave amplitudes are close to the saturation level. In general, the wave refraction leads to more fast wave breaking than that in the 2‐D case. As a results, it should be expected to find localized regions of higher levels of water mixing and turbulence in the vicinity of local banks and headlands where LAIWs produce concave patterns. The areas of local bottom depressions, on the contrary, should be considered as potential places with lower level of background mixing.
Representer‐based variational data assimilation in a nonlinear model of nearshore circulation
Authors: Kurapov Alexander L. , Egbert Gary D. , Allen J. S. , Miller Robert N.
Published: November 2007

A representer‐based variational data assimilation (DA) method is implemented with a shallow‐water model of circulation in the nearshore surf zone and tested with synthetic data. The behavior of the DA system is evaluated over a 1‐hour time interval that is large compared to timescales characteristic of instability growth and eddy interactions. True reference solutions, from which the synthetic data are sampled, correspond to fully developed unsteady nonlinear flows driven by a steady spatially varying forcing representing the effect of breaking waves. Forcing and initial conditions are adjusted to fit the data. The convergence of the nonlinear optimization algorithm and the accuracy of the forcing and state estimates depend on the choice of the forcing error covariance C. In a weakly nonlinear (equilibrated waves) regime, using C that allows only a steady forcing correction yields a convergent and accurate solution. In a more strongly nonlinear regime, the DA system cannot find sufficient degrees of freedom in the steady forcing to control eddy variability. Implementing a bell‐shaped temporal correlation function in C with the 1‐min decorrelation scale yields a convergent linearized inverse solution that describes correctly the spatiotemporal variability in the eddy field. The corresponding estimate of forcing, however, is not satisfactory. Accurate estimates of both the flow and the forcing can be achieved by implementing a composite C with a temporal correlation separated into an O(1) steady and small amplitude time‐variable parts.
Mesoscale covariance of transport and CO2 fluxes: Evidence from observations and simulations using the WRF‐VPRM coupled atmosphere‐biosphere model
Authors: Ahmadov R. , Gerbig C. , Kretschmer R. , Koerner S. , Neininger B. , Dolman A. J. , Sarrat C.
Published: November 2007

We developed a modeling system which combines a mesoscale meteorological model, the Weather Research and Forecasting (WRF) model, with a diagnostic biospheric model, the Vegetation Photosynthesis and Respiration (VPRM). The WRF‐VPRM modeling system was designed to realistically simulate high‐resolution atmospheric CO2 concentration fields. In the system, WRF takes into account anthropogenic and biospheric CO2 fluxes and realistic initial and boundary conditions for CO2 from a global model. The system uses several “tagged” tracers for CO2 fields from different sources. VPRM uses meteorological fields from WRF and high‐resolution satellite indices to simulate biospheric CO2 fluxes with realistic spatiotemporal patterns. Here we present results from the application of the model for interpretation of measurements made within the CarboEurope Regional Experiment Strategy (CERES). Simulated fields of meteorological variables and CO2 were compared against ground‐based and airborne observations. In particular, the characterization by aircraft measurements turned out to be crucial for the model evaluation. The comparison revealed that the model is able to capture the main observed features in the CO2 distribution reasonably well. The simulations showed that daytime CO2 measurements made at coastal stations can be strongly affected by land breeze and subsequent sea breeze transport of CO2 respired from the vegetation during the previous night, which can lead to wrong estimates when such data are used in inverse studies. The results also show that WRF‐VPRM is an effective modeling tool for addressing the near‐field variability of CO2 fluxes and concentrations for observing stations around the globe.
Scattering of ELF waves by underground formations because of night‐day ionospheric ridge
Authors: Valagiannopoulos C. A. , Uzunoglu N. K.
Published: November 2007

In the present work the variation in ionospheric height observed during the dawn or dusk hours is used to develop an electromagnetic imaging system for extremely low frequencies (ELF). The description concerns the mathematical principles of the proposed method rather than a realistic implementation of the technique. The scattering of ELF waves emanating from a point source on the Earth surface by a cylindrical underground formation is studied analytically with use of a Green's function method. The ionospheric discontinuity is treated with the help of mode matching technique and the subterranean scatterer by application of the method of auxiliary sources. Numerical results are presented and discussed for several cases.
Newspaper reporting of space weather: End of a golden age
Authors: Odenwald Sten
Published: November 2007

The reporting of the human impacts of space weather phenomena as a significant American newspaper story has passed through a golden age, which ended just after World War II. Prior to this time, significant geomagnetic storms and solar flare events were reported in considerable detail, with specific references made to actual impacts to telegraph, wireless, and radio communications systems among others. After World War II, news stories shrank dramatically in terms of the size of the article, the location of the story in the newspaper, and the number of items mentioned in the article. This paper is an historical analysis of the scope of newspaper reporting on 52 major storms with AA* > 170 occurring in American newspapers since 1870 and the changing trends in how the events were covered. I will show that even before the advent of news reporting on the World Wide Web, there was a precipitous decline in space weather reporting during the postwar period from ca. 1945–1990. The reason for this decline is not immediately obvious, but a few suggestions will be provided. I also publish 141 excerpts from the newspaper sample highlighting a variety of “human impacts” caused by this complete sample of storm events, along with a small collection of interesting illustrations that accompanied a few of the articles.
Effects of aboveground grazing on coupling among nitrifier activity, abundance and community structure
Authors: Le Roux Xavier , Poly Franck , Currey Pauline , Commeaux Claire , Hai Brigitte , Nicol Graeme W , Prosser James I , Schloter Michael , Attard Eléonore , Klumpp Katja
Published: November 2007

The influence of switches in grassland management to or from grazing on the dynamics of nitrifier activity, as well as the abundance of ammonia-oxidizing bacteria, AOB and ammonia-oxidizing archeae, AOA, was analyzed for two years after changing management. Additionally community structure of AOB was surveyed. Four treatments were compared in mesocosms: grazing on previously grazed grassland (G-G); no grazing on ungrazed grassland (U-U); grazing on ungrazed grassland (U-G) and cessation of grazing on grazed grassland (G-U). Nitrifier activity and abundance were always higher for G-G than U-U treatments and AOB community structure differed between these treatments. AOA abundance was in the same range as AOB abundance and followed the same trend. Grazing led to a change in AOB community structure within <5 months and a subsequent (5–12 months) increase in nitrifier activity and abundance. In contrast, cessation of grazing led to a decrease in nitrifier activity and abundance within <5 months and to a later (5–12 months) change in AOB community structure. Activity in G-U and U-G was similar to that in U-U and G-G, respectively, after 12 months. Sequence analysis of 16S rRNA gene clones showed that AOB retrieved from soils fell within the Nitrosospira lineage and percentages of AOB related to known Nitrosospira groups were affected by grazing. These results demonstrate that AOB and AOA respond quickly to changes in management. The selection of nitrifiers adapted to novel environmental conditions was a prerequisite for nitrification enhancement in U-G, whereas nitrification decrease in G-U was likely due to a partial starvation and decrease in the abundance of nitrifiers initially present. The results also suggest that taxonomic affiliation does not fully infer functional traits of AOB.
A novel DSF-like signal from Burkholderia cenocepacia interferes with Candida albicans morphological transition
Authors: Boon Calvin , Deng Yinyue , Wang Lian-Hui , He Yawen , Xu Jin-Ling , Fan Yang , Pan Shen Q , Zhang Lian-Hui
Published: November 2007

In addition to producing lethal antibiotics, microorganisms may also use a new form of antagonistic mechanism in which signal molecules are exported to influence the gene expression and hence the ecological competence of their competitors. We report here the isolation and characterization of a novel signaling molecule, cis-2-dodecenoic acid (BDSF), from Burkholderia cenocepacia. BDSF is structurally similar to the diffusible signal factor (DSF) that is produced by the RpfF enzyme of Xanthomonas campestris. Deletion analysis demonstrated that Bcam0581, which encodes an RpfF homologue, was essential for BDSF production. The gene is highly conserved and widespread in the Burkholderia cepacia complex. Exogenous addition of BDSF restored the biofilm and extracellular polysaccharide production phenotypes of Xanthomonas campestris pv. campestris DSF-deficient mutants, highlighting its potential role in inter-species signaling. Further analyses showed that Candida albicans germ tube formation was strongly inhibited by either coculture with B. cenocepacia or by exogenous addition of physiological relevant levels of BDSF, whereas deletion of Bcam0581 abrogated the inhibitory ability of the bacterial pathogen. As B. cenocepacia and C. albicans are frequently encountered human pathogens, identification of the BDSF signal and its activity thus provides a new insight into the molecular grounds of their antagonistic interactions whose importance to microbial ecology and pathogenesis is now becoming evident.
Multidimensional structure of stream flow regime in a hierarchy of landscapes within the U.S. Great Lakes basin
Authors: Shmagin Boris , Johnston Carol , Bridgham Scott
Published: November 2007

Stream flow data were used to evaluate a landscape hierarchy ranging from the Ontonagon River watershed (OW) to the upper peninsula of Michigan (MUP) to the entire Great Lakes basin (GLB). Flow records (1926-1988) were obtained for 45 USGS gauging stations within the GLB with drainage areas of 100-1450 sq. mi. Data were arranged in five initial matrixes with number of time series from 14 to 45. Factor analysis of average annual flow revealed from three to six patterns of stream runoff within distinct regions of the GLB. A typical watershed was selected to represent each of the five distinct regions identified for the period 1956-88, and its data were used to analyze monthly average flow values. This analysis identified two to five groupings of months with similar flow characteristics. For each annual time series of the typical five stream flow patterns of GLB regression equations were obtained from fore main indices of global atmospheric circulation. A similar analysis was completed for MUP and OW. Multilevel and multidimensional time spatial structure was discovered with factor as axis within landscape units as a homogeneous field. This kind of structure allows direct and more precise research for similar structures in atmosphere circulation and atmosphere-hydrosphere connections and regimes for entire GLB and its parts.
Determination of single living cell’s dry/water mass using optofluidic chip
Authors: Song W. Z. , Liu A. Q. , Swaminathan S. , Lim C. S. , Yap P. H. , Ayi T. C.
Published: November 2007

This paper presents an interferometric method for measuring the dry/wet mass of a single living cell using an optofluidic chip. It consists of the fiber Mach-Zehnder interferometer and the fiber-optical trap, both of which are integrated onto a single chip. In experiment, a single living cell is captured by the fiber-optical trap, and then the cell’s refractive index and diameter are simultaneously determined by the spectral shift in response to the buffer modulation. Hence, both cell dry and water masses can be calculated with a precision higher than 5%.
Noninvasive method to measure the ion flux in capacitive discharge
Authors: Lee Min-Hyong , Lee Hyo-Chang , Chung Chin-Wook
Published: November 2007

A noninvasive method to measure the ion flux from the current flowing through the substrate (substrate current) in a capacitive discharge is proposed. The substrate current consists of a displacement current and a conduction current. In a high frequency capacitively coupled plasma, the displacement current is usually much higher than the conduction current. However, the displacement current becomes negligible at a moment that the second time derivative of the substrate current becomes zero (the first time derivative reaches its minimum), and from the measured substrate current at that time, the ion flux can be obtained. The measured ion flux from this method is compared with the flux measured by another diagnostic method.
A double-band high-power microwave source
Authors: Fan Yu-Wei , Zhong Hui-Huang , Li Zhi-Qiang , Shu Ting , Zhang Jian-De , Zhang Jun , Zhang Xiao-Ping , Yang Jian-Hua , Luo Ling
Published: November 2007

In order to increase the power conversion efficiency of a magnetically insulated line oscillator (MILO), an axially extracted virtual cathode oscillator (VCO) is introduced to utilize the load current in the MILO, so it is called the MILO-VCO. In this device, the MILO and VCO are operated synchronously and generate high-power microwaves. The MILO-VCO is investigated in detail with particle-in-cell (PIC) methods (KARAT code). In simulation, the diode voltage is 640 kV and the current is 50 kA. The total peak power of the MILO-VCO is 5.22 GW and the corresponding power conversion efficiency is 16.3%. In the MILO-VCO, the peak power of the MILO is 3.91 GW and its frequency is 1.76 GHz; the peak power of the VCO is 1.33 GW and its frequency is 3.79 GHz.
Controlling four-wave and six-wave mixing processes in multilevel atomic systems
Authors: Zhang Yanpeng , Khadka Utsab , Anderson Blake , Xiao Min
Published: November 2007

We experimentally demonstrate that four-wave mixing (FWM) and six-wave mixing (SWM) processes can be selectively turned on and off in a close-cycled four-level atomic system. Under certain laser beam configuration, the FWM and SWM processes can be made to coexist with similar signal amplitudes and transmit through the same electromagnetically induced transparency window in such folded four-level atomic system. By introducing an additional pumping laser beam connecting to the fifth energy level, both FWM and SWM signals can be greatly enhanced.
Three-dimensional tracking of individual quantum dots
Authors: Lessard Guillaume A. , Goodwin Peter M. , Werner James H.
Published: November 2007

We describe an instrument that extends the state of the art in a single-molecule tracking technology, allowing extended observations of single fluorophores and fluorescently labeled proteins as they undergo directed and diffusive transport in three dimensions. We demonstrate three-dimensional tracking of individual quantum dots undergoing diffusion for durations of over a second at velocities comparable to those of intracellular signaling processes.
Single-photon interferography in InAs∕InP quantum dots emitting at 1300nm wavelength
Authors: Kuroda T. , Sakuma Y. , Sakoda K. , Takemoto K. , Usuki T.
Published: November 2007

Photoluminescence from a single InAs∕InP quantum dot emitting at a wavelength of 1300nm is analyzed by the interferography technique. The first-order correlation function was measured for emission signals from an isolated quantum dot with continuous wave photoexcitation. The spectral shape was evaluated by Fourier transform of the correlation function, revealing the contributions of Lorentzian and Gaussian functions. The Lorentzian homogeneous width was determined to be 28(±4)μeV at 8K.
Dominant role of tunneling resistance in the electrical conductivity of carbon nanotube–based composites
Authors: Li Chunyu , Thostenson Erik T. , Chou Tsu-Wei
Published: November 2007

The effect of nanotube/nanotube contact resistance on the electrical conductivity of carbon nanotube–based nanocomposites is studied. The tunneling resistance due to an insulating film of matrix material between crossing nanotubes is calculated by assuming a rectangular potential barrier in the insulating film. Monte Carlo simulations indicate that the tunneling resistance plays a dominant role in the electrical conductivity of composites, and the maximum tunneling distance is found to be about 1.8nm. Electrical conductivities of composites with inplane random distributions of carbon nanotubes follow the scaling law and the critical exponent depends on the level of contact resistance.
Regulation of spine morphology and spine density by NMDA receptor signaling
in vivo
Authors: Ultanir Sila K. , Kim Ji-Eun , Hall Benjamin J. , Deerinck Thomas , Ellisman Mark , Ghosh Anirvan
Published: November 2007

Dendritic spines are the major sites of excitatory synaptic transmission in the CNS, and their size and density influence the functioning of neuronal circuits. Here we report that NMDA receptor signaling plays a critical role in regulating spine size and density in the developing cortex. Genetic deletion of the NR1 subunit of the NMDA receptor in the cortex leads to a decrease in spine density and an increase in spine head size in cortical layer 2/3 pyramidal neurons. This process is accompanied by an increase in the presynaptic axon bouton volume and the postsynaptic density area, as well as an increase in the miniature excitatory postsynaptic current amplitude and frequency. These observations indicate that NMDA receptors regulate synapse structure and function in the developing cortex.
Mitochondrial origin-binding protein UMSBP mediates DNA replication and segregation in trypanosomes
Authors: Milman Neta , Motyka Shawn A. , Englund Paul T. , Robinson Derrick , Shlomai Joseph
Published: November 2007

Kinetoplast DNA (kDNA) is the remarkable mitochondrial genome of trypanosomatids. Its major components are several thousands of topologically linked DNA minicircles, whose replication origins are bound by the universal minicircle sequence-binding protein (UMSBP). The cellular function of UMSBP has been studied in
Trypanosoma brucei
by using RNAi analysis. Silencing of the trypanosomal
UMSBP
genes resulted in remarkable effects on the trypanosome cell cycle. It significantly inhibited the initiation of minicircle replication, blocked nuclear DNA division, and impaired the segregation of the kDNA network and the flagellar basal body, resulting in growth arrest. These observations, revealing the function of UMSBP in kDNA replication initiation and segregation as well as in mitochondrial and nuclear division, imply a potential role for UMSBP in linking kDNA replication and segregation to the nuclear S-phase control during the trypanosome cell cycle.
ID
genes mediate tumor reinitiation during breast cancer lung metastasis
Authors: Gupta Gaorav P. , Perk Jonathan , Acharyya Swarnali , de Candia Paola , Mittal Vivek , Todorova-Manova Katia , Gerald William L. , Brogi Edi , Benezra Robert , Massagué Joan
Published: November 2007

The establishment of distant metastases depends on the capacity of small numbers of cancer cells to regenerate a tumor after entering a target tissue. The mechanisms that confer this capacity remain to be defined. Here we identify a role for the transcriptional inhibitors of differentiation Id1 and Id3 as selective mediators of lung metastatic colonization in the triple negative [TN, i.e., lacking expression of estrogen receptor and progesterone receptor, and lacking Her2 (human epidermal growth factor receptor 2) amplification] subgroup of human breast cancer. Although broad expression of Id1 has recently been documented in tumors of the rare metaplastic subtype, here we report that rare Id1-expressing cells are also present in the more common TN subset of human breast tumors but not in other subtypes. We also provide evidence that Id1 expression is enriched in clinically obtained hormone receptor negative lung metastases. Functional studies demonstrate that Id1 and its closely related family member Id3 are required for tumor initiating functions, both in the context of primary tumor formation and during metastatic colonization of the lung microenvironment.
In vivo
characterization of lung metastatic progression reveals that Id1 and Id3 facilitate sustained proliferation during the early stages of metastatic colonization, subsequent to extravasation into the lung parenchyma. These results shed light on the proliferative mechanisms that initiate metastatic colonization, and they implicate Id1 and Id3 as mediators of this malignant function in the TN subgroup of breast cancers.
Axial ligand tuning of a nonheme iron(IV)–oxo unit for hydrogen atom abstraction
Authors: Sastri Chivukula V. , Lee Jimin , Oh Kyungeun , Lee Yoon Jin , Lee Junghyun , Jackson Timothy A. , Ray Kallol , Hirao Hajime , Shin Woonsup , Halfen Jason A. , Kim Jinheung , Que Lawrence , Shaik Sason , Nam Wonwoo
Published: November 2007

The reactivities of mononuclear nonheme iron(IV)–oxo complexes bearing different axial ligands, [Fe
IV
(O)(TMC)(X)]
n+
[where TMC is 1,4,8,11-tetramethyl-1,4,8,11-tetraazacyclotetradecane and X is NCCH
3
(1-NCCH
3
), CF
3
COO
−
(1-OOCCF
3
), or N
3
−
(1-N
3
)], and [Fe
IV
(O)(TMCS)]
+
(1′-SR) (where TMCS is 1-mercaptoethyl-4,8,11-trimethyl-1,4,8,11-tetraazacyclotetradecane), have been investigated with respect to oxo-transfer to PPh
3
and hydrogen atom abstraction from phenol O

H and alkylaromatic C

H bonds. These reactivities were significantly affected by the identity of the axial ligands, but the reactivity trends differed markedly. In the oxidation of PPh
3
, the reactivity order of 1-NCCH
3
> 1-OOCCF
3
> 1-N
3
> 1′-SR was observed, reflecting a decrease in the electrophilicity of iron(IV)–oxo unit upon replacement of CH
3
CN with an anionic axial ligand. Surprisingly, the reactivity order was inverted in the oxidation of alkylaromatic C

H and phenol O

H bonds, i.e., 1′-SR > 1-N
3
> 1-OOCCF
3
> 1-NCCH
3
. Furthermore, a good correlation was observed between the reactivities of iron(IV)–oxo species in H atom abstraction reactions and their reduction potentials,
E
p,c
, with the most reactive 1′-SR complex exhibiting the lowest potential. In other words, the more electron-donating the axial ligand is, the more reactive the iron(IV)–oxo species becomes in H atom abstraction. Quantum mechanical calculations show that a two-state reactivity model applies to this series of complexes, in which a triplet ground state and a nearby quintet excited-state both contribute to the reactivity of the complexes. The inverted reactivity order in H atom abstraction can be rationalized by a decreased triplet-quintet gap with the more electron-donating axial ligand, which increases the contribution of the much more reactive quintet state and enhances the overall reactivity.
Mechanoenzymes under superstall and large assisting loads reveal structural features
Authors: Tsygankov Denis , Fisher Michael E.
Published: November 2007

Single-molecule experiments on the motor protein kinesin have observed runs of backsteps and thus a negative, that is,
reverse
mean velocity,
V
, under superstall loads,
F
; but, counterintuitively, beyond stall,
V
(
F
) displays a shallow
minimum
and then
decreases
in magnitude. Conversely, under
assisting
loads
V
(
F
) rises to a
maximum
before decreasing monotonically. By contrast, while the velocity of myosin V also saturates under assisting loads, the motor moves backward increasingly rapidly under superstall loads. For both kinesin and myosin V this behavior is implied remarkably well by simple two-state kinetic models when extrapolated to large loads. To understand the origins of such results in general mechanoenzymes, biochemical kinetic descriptions are discussed on the basis of a free-energy landscape picture. It transpires that the large-load performance is determined by the geometrical placement of the intermediate mechanochemical states of the enzymatic cycles relative to the associated transition states. Explicit criteria are presented for
N
-state sequential kinetics, including side-reaction chains, etc., and for parallel-pathway models. Physical colocalization of biochemically distinct states generally implies large-load velocity saturation.
Transmembrane Domain Interactions Control Biological Functions of Neuropilin-1
Authors: Roth Lise , Nasarre Cécile , Dirrig-Grosch Sylvie , Aunis Dominique , Crémel Gérard , Hubert Pierre , Bagnard Dominique
Published: November 2007

Neuropilin-1 (NRP1) is a transmembrane receptor playing a pivotal role in the control of semaphorins and VEGF signaling pathways. The exact mechanism controlling semaphorin receptor complex formation is unknown. A structural analysis and modeling of NRP1 revealed a putative dimerization GxxxG motif potentially important for NRP1 dimerization and oligomerization. Our data show that this motif mediates the dimerization of the transmembrane domain of NRP1 as demonstrated by a dimerization assay (ToxLuc assay) performed in natural membrane and FRET analysis. A synthetic peptide derived from the transmembrane segment of NRP1 abolished the inhibitory effect of Sema3A. This effect depends on the capacity of the peptide to interfere with NRP1 dimerization and the formation of oligomeric complexes. Mutation of the GxxxG dimerization motif in the transmembrane domain of NRP1 confirmed its biological importance for Sema3A signaling. Overall, our results shed light on an essential step required for semaphorin signaling and provide novel evidence for the crucial role of transmembrane domain of bitopic protein containing GxxxG motif in the formation of receptor complexes that are a prerequisite for cell signaling.
B-RAF Regulation of Rnd3 Participates in Actin Cytoskeletal and Focal Adhesion Organization
Authors: Klein R. Matthew , Spofford Laurie S. , Abel Ethan V. , Ortiz Arisa , Aplin Andrew E.
Published: November 2007

The actin cytoskeleton controls multiple cellular functions, including cell morphology, movement, and growth. Accumulating evidence indicates that oncogenic activation of the mitogen-activated protein kinase kinase/extracellular signal-regulated kinase 1/2 (MEK/ERK1/2) pathway is accompanied by actin cytoskeletal reorganization. However, the signaling events contributing to actin cytoskeleton remodeling mediated by aberrant ERK1/2 activation are largely unknown. Mutant B-RAF is found in a variety of cancers, including melanoma, and it enhances activation of the MEK/ERK1/2 pathway. We show that targeted knockdown of B-RAF with small interfering RNA or pharmacological inhibition of MEK increased actin stress fiber formation and stabilized focal adhesion dynamics in human melanoma cells. These effects were due to stimulation of the Rho/Rho kinase (ROCK)/LIM kinase-2 signaling pathway, cumulating in the inactivation of the actin depolymerizing/severing protein cofilin. The expression of Rnd3, a Rho antagonist, was attenuated after B-RAF knockdown or MEK inhibition, but it was enhanced in melanocytes expressing active B-RAF. Constitutive expression of Rnd3 suppressed the actin cytoskeletal and focal adhesion effects mediated by B-RAF knockdown. Depletion of Rnd3 elevated cofilin phosphorylation and stress fiber formation and reduced cell invasion. Together, our results identify Rnd3 as a regulator of cross talk between the RAF/MEK/ERK and Rho/ROCK signaling pathways, and a key contributor to oncogene-mediated reorganization of the actin cytoskeleton and focal adhesions.
KNL1 and the CENP-H/I/K Complex Coordinately Direct Kinetochore Assembly in Vertebrates
Authors: Cheeseman Iain M. , Hori Tetsuya , Fukagawa Tatsuo , Desai Arshad
Published: November 2007

Chromosome segregation during mitosis requires the assembly of a large proteinaceous structure termed the kinetochore. In Caenorhabditis elegans, KNL-1 is required to target multiple outer kinetochore proteins. Here, we demonstrate that the vertebrate KNL1 counterpart is essential for chromosome segregation and is required to localize a subset of outer kinetochore proteins. However, unlike in C. elegans, depletion of vertebrate KNL1 does not abolish kinetochore localization of the microtubule-binding Ndc80 complex. Instead, we show that KNL1 and CENP-K, a subunit of a constitutively centromere-associated complex that is missing from C. elegans, coordinately direct Ndc80 complex localization. Simultaneously reducing both hKNL1 and CENP-K function abolishes all aspects of kinetochore assembly downstream of centromeric chromatin and causes catastrophic chromosome segregation defects. These findings explain discrepancies in kinetochore assembly pathways between different organisms and reveal a surprising plasticity in the assembly mechanism of an essential cell division organelle.
Identification of lactobacilli by pheS and rpoA gene sequence analyses
Authors: Naser Sabri M. , Dawyndt Peter , Hoste Bart , Gevers Dirk , Vandemeulebroecke Katrien , Cleenwerck Ilse , Vancanneyt Marc , Swings Jean
Published: November 2007

The aim of this study was to evaluate the use of the phenylalanyl-tRNA synthase alpha subunit (pheS) and the RNA polymerase alpha subunit (rpoA) partial gene sequences for species identification of members of the genus Lactobacillus. Two hundred and one strains representing the 98 species and 17 subspecies were examined. The pheS gene sequence analysis provided an interspecies gap, which in most cases exceeded 10 % divergence, and an intraspecies variation of up to 3 %. The rpoA gene sequences revealed a somewhat lower resolution, with an interspecies gap normally exceeding 5 % and an intraspecies variation of up to 2 %. The combined use of pheS and rpoA gene sequences offers a reliable identification system for nearly all species of the genus Lactobacillus. The pheS and rpoA gene sequences provide a powerful tool for the detection of potential novel Lactobacillus species and synonymous taxa. In conclusion, the pheS and rpoA gene sequences can be used as alternative genomic markers to 16S rRNA gene sequences and have a higher discriminatory power for reliable identification of species of the genus Lactobacillus.
Howardella ureilytica gen. nov., sp. nov., a Gram-positive, coccoid-shaped bacterium from a sheep rumen
Authors: Cook Anthony R. , Riley Paul W. , Murdoch Heather , Evans Paul N. , McDonald Ian R.
Published: November 2007

An unidentified obligately anaerobic, fastidious, Gram-positive, non-motile, non-spore-forming, non-fermentative coccoid-shaped bacterium (designated strain GPC 589T) was isolated from the rumen fluid of a sheep. The major fatty acid constituents (>5 %) were C16 : 0(29.2 %), C18 : 0(40.7 %) and an unidentified compound (19.7 %) with an equivalent chain-length of 13.523. The G+C content of the DNA was 34 mol%. The organism was strongly ureolytic and generated ATP through the hydrolysis of urea. Comparative 16S rRNA gene sequence analysis demonstrated that strain GPC 589Twas far removed, phylogenetically, from the ruminococci and related Gram-positive anaerobic cocci but exhibited a phylogenetic association withClostridiumrRNA cluster XIVa [as defined by Collins, M. D., Lawson, P. A., Willems, A., Cordoba, J. J., Fernandez-Garayzabal, J., Garcia, P., Cai, J., Hippe, H. & Farrow, J. A. E. (1994).Int J Syst Bacteriol44, 812–826]. Sequence divergence values of 12.5 % or more were observed between strain GPC 589Tand all other recognized species within this and related rRNA clostridial clusters. Phylogenetic analysis showed that strain GPC 589Trepresents a new genus within cluster XIVa. On the basis of both phylogenetic and phenotypic evidence, it is proposed that strain GPC 589Tshould be classified as representing a new genus and novel species,Howardella ureilyticagen. nov., sp. nov. The type strain is strain GPC 589T(=DSM 15118T=JCM 13267T).
Leucobacter chromiireducens subsp. solipictus subsp. nov., a pigmented bacterium isolated from the nematode Caenorhabditis elegans, and emended description of L. chromiireducens
Authors: Muir Rachel E. , Tan Man-Wah
Published: November 2007

A yellow-pigmented, Gram-positive, aerobic, non-motile, non-spore-forming, irregular rod-shaped bacterium (strain TAN 31504T) was isolated from the bacteriophagous nematodeCaenorhabditis elegans. Based on 16S rRNA gene sequence similarity, DNA G+C content of 69.5 mol%, 2,4-diaminobutyric acid in the cell-wall peptidoglycan, major menaquinone MK-11, abundance of anteiso- and iso-fatty acids, polar lipids diphosphatidylglycerol and phosphatidylglycerol and a number of shared biochemical characteristics, strain TAN 31504Twas placed in the genusLeucobacter. DNA–DNA hybridization comparisons demonstrated a 91 % DNA–DNA relatedness between strain TAN 31504TandLeucobacter chromiireducensLMG 22506Tindicating that these two strains belong to the same species, when the recommended threshold value of 70 % DNA–DNA relatedness for the definition of a bacterial species by the ad hoc committee on reconciliation of approaches to bacterial systematics is considered. Based on distinct differences in morphology, physiology, chemotaxonomic markers and various biochemical characteristics, it is proposed to split the speciesL. chromiireducensinto two novel subspecies,Leucobacter chromiireducenssubsp.chromiireducenssubsp. nov. (type strain L-1T=CIP 108389T=LMG 22506T) andLeucobacter chromiireducenssubsp.solipictussubsp. nov. (type strain TAN 31504T=DSM 18340T=ATCC BAA-1336T).
Arenimonas malthae sp. nov., a gammaproteobacterium isolated from an oil-contaminated site
Authors: Young Chiu-Chung , Kämpfer Peter , Ho Mann-Jing , Busse Hans-Jürgen , Huber Birgit E. , Arun A. B. , Shen Fo-Ting , Lai Wei-An , Rekha P. D.
Published: November 2007

A Gram-negative, rod-shaped bacterium (CC-JY-1T) was isolated on nutrient agar from a soil sample collected from an oil-contaminated site located in Chyai county, Taiwan. 16S rRNA gene sequence analysis demonstrated that this isolate is unique, showing 96.7 % sequence similarity to the type strain of Arenimonas donghaensis and similarities of 93.0–93.8 % to species of the genera Thermomonas, Lysobacter and Silanimonas. The presence of ubiquinone Q-8, a polar lipid profile consisting of the major compounds diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine and the fatty acid profile were in accordance with the phylogenetic affiliation of CC-JY-1T. DNA–DNA reassociation experiments between CC-JY-1T and A. donghaensis KACC 11381T resulted in a mean relatedness value of 32 %, indicating that strain CC-JY1T represents a novel species in the genus Arenimonas, for which we propose the name Arenimonas malthae sp. nov. The type strain is CC-JY-1T (=CCUG 53596T =CIP 109310T).
Rhodanobacter
ginsengisoli sp. nov. and Rhodanobacter
terrae sp. nov., isolated from soil cultivated with Korean ginseng
Authors: Weon Hang-Yeon , Kim Byung-Yong , Hong Seung-Beom , Jeon Young-Ah , Kwon Soon-Wo , Go Seung-Joo , Koo Bon-Sung
Published: November 2007

Two bacterial isolates from ginseng fields in Korea, strains GR17-7T and GP18-1T, were characterized using a polyphasic approach. Phylogenetic analysis of their 16S rRNA gene sequences revealed a clear affiliation with the Gammaproteobacteria, and showed that the closest phylogenetic relationships were with members of the genus Rhodanobacter. The 16S rRNA gene sequence similarity between strains GR17-7T and GP18-1T was 97.2 %. Both strains showed 16S rRNA gene sequence similarities of 95.2–96.9 % to type strains of recognized Rhodanobacter species. The G+C contents of the DNA of strains GR17-7T and GP18-1T were 61.0 and 62.5 mol%, respectively. According to the DNA–DNA hydridization tests, the hybridization value between strains GR17-7T and GP18-1T was 34 %. Strains GR17-7T and GP18-1T showed less than 32 % DNA–DNA relatedness with Rhodanobacter fulvus KCTC 12098T and Rhodanobacter spathiphylli LMG 23181T. Strains GR17-7T and GP18-1T were aerobic, Gram-negative, rod-shaped, and catalase- and oxidase-positive. Major fatty acids of both strains were iso-C17 : 1
ω9c and iso-C16 : 0. Based on the data presented, two novel Rhodanobacter species are proposed, with the names Rhodanobacter ginsengisoli sp. nov. (type strain GR17-7T=KACC 11762T=DSM 18993T) and Rhodanobacter terrae sp. nov. (type strain GP18-1T=KACC 11761T=DSM 19241T).
Desulfotignum toluenicum sp. nov., a novel toluene-degrading, sulphate-reducing bacterium isolated from an oil-reservoir model column
Authors: Ommedal Hege , Torsvik Terje
Published: November 2007

A Gram-negative, sulphate-reducing bacterium (strain H3T) was isolated from an oil-reservoir model column. The new isolate was able to oxidize toluene coupled to hydrogen sulphide production. For growth, the optimum salt concentration was 1.5 % (w/v), the optimum pH was 7.2 and the optimum temperature was 34 °C. The cells were straight to slightly curved rods, 0.6–1.0 μm in diameter and 1.4–2.5 μm in length. The predominant fatty acids were C16 : 0, C16 : 1
ω7c and C17 : 0 cyclo, and the cells also contained dimethylacetals. Cloning and sequencing of a 1505 bp long fragment of the 16S rRNA gene showed that strain H3T is a member of the Deltaproteobacteria and is related closely to Desulfotignum balticum DSM 7044T. The G+C content of the DNA was 52.0 mol% and the DNA–DNA similarity to D. balticum DSM 7044T was 56.1 %. Based on differences in DNA sequence and the unique property of toluene degradation, it is proposed that strain H3T should be designated a member of a novel species within the genus Desulfotignum, for which the name Desulfotignum toluenicum sp. nov. is proposed. The type strain is H3T (=DSM 18732T=ATCC BAA-1460T).
Lechevalieria xinjiangensis sp. nov., a novel actinomycete isolated from radiation-polluted soil in China
Authors: Wang Wei , Zhang Zhidong , Tang Qiyong , Mao Jun , Wei Dong , Huang Ying , Liu Zhiheng , Shi Yuhu , Goodfellow Michael
Published: November 2007

A novel actinomycete was isolated from radiation-polluted soil collected from Xinjiang in north-western China. The isolate, strain R24T, was found to have chemical and morphological properties associated with members of the genusLechevalieria. An almost-complete 16S rRNA gene sequence of the isolate was aligned with corresponding sequences from representatives of the genusLechevalieriaand related taxa, using three tree-making algorithms, and was shown to form a distinct phyletic line in theLechevalieriaphylogenetic tree. DNA–DNA relatedness and phenotypic data served to distinguish strain R24Tfrom members of the threeLechevalieriaspecies with validly published names. The genotypic and phenotypic data show that the isolate should be classified as a novel species within the genusLechevalieria. The name proposed for this taxon isLechevalieria xinjiangensissp. nov. The type strain is R24T(=CGMCC 4.3525T=DSM 45081T).
Chitinilyticum aquatile gen. nov., sp. nov., a chitinolytic bacterium isolated from a freshwater pond used for Pacific white shrimp culture
Authors: Chang Shu-Chen , Chen Wen-Ming , Wang Jih-Terng , Wu Ming-Chang
Published: November 2007

Strain c14T, originally isolated from surface water of a freshwater pond located in Pingtung (southern Taiwan) used for culture of Pacific white shrimp (Litopenaeus vannamei), was subjected to a polyphasic taxonomic approach. The strain exhibited strong chitinolytic activity and was able to grow under aerobic and anaerobic conditions by utilizing chitin exclusively as the carbon, nitrogen and energy source. Phylogenetic analysis of the 16S rRNA gene sequence revealed a clear affiliation of the proposed bacterium to the Betaproteobacteria, most closely related to Chitinibacter tainanensis S1T, Deefgea rivuli WB 3.4-79T and Silvimonas terrae KM-45T, with 94.6, 93.6 and 92.9 % 16S rRNA gene sequence similarity, respectively. The predominant fatty acids detected in cells of strain c14T were C16 : 0, C18 : 1
ω7c and summed feature 3 (C16 : 1
ω7c and/or C15 : 0 iso 2-OH). The G+C content of the genomic DNA was 69.5 (±1.0) mol%. Biochemical, physiological, chemotaxonomic and phylogenetic analyses showed that strain c14T could not be assigned to any known genus of the Betaproteobacteria. Therefore, strain c14T is classified within a novel genus and species, for which the name Chitinilyticum aquatile gen. nov., sp. nov. is proposed. The type strain of Chitinilyticum aquatile is c14T (=LMG 23346T =BCRC 17533T).
Maribacter polysiphoniae sp. nov., isolated from a red alga
Authors: Nedashkovskaya Olga I. , Vancanneyt Marc , De Vos Paul , Kim Seung Bum , Lee Myung Sook , Mikhailov Valery V.
Published: November 2007

A novel gliding, heterotrophic, Gram-negative, yellow–orange-pigmented, aerobic, oxidase- and catalase-positive bacterium, designated strain KMM 6151T, was isolated from the Pacific red alga Polysiphonia japonica. Analysis of the 16S rRNA gene sequence of the strain revealed that it formed a distinct lineage within the genus Maribacter, family Flavobacteriaceae, with sequence similarities in the range 94.6–96.9 %. On the basis of phenotypic, genotypic and phylogenetic data, strain KMM 6151T represents a novel species of the genus Maribacter, for which the name Maribacter polysiphoniae sp. nov. is proposed. The type strain is KMM 6151T (=KCTC 22021T=LMG 23671T).
Shewanella haliotis sp. nov., isolated from the gut microflora of abalone, Haliotis discus hannai
Authors: Kim Duwoon , Baik Keun Sik , Kim Mi Sun , Jung Bok-Mi , Shin Tai-Sun , Chung Gyu-Hwa , Rhee Moon Soo , Seong Chi Nam
Published: November 2007

A motile, rod-shaped, pink–orange pigmented bacterium, designated strain DW01T, was isolated from the gut microflora of abalone collected from the South Sea (Republic of Korea). Cells were Gram-negative, facultatively anaerobic, catalase- and oxidase-positive. The major fatty acids were iso-C15 : 0(17.7 %), C16 : 0(13.4 %), iso-C15 : 02-OH and/or C16 : 1ω7c(12.5 %) and C17 : 1ω8c(10.7 %). The DNA G+C content was 53.7 mol%. A phylogenetic tree based on the 16S rRNA gene sequences showed that strain DW01Tforms a lineage of the genusShewanellaand is closely related toShewanella algaeATCC 51192T(98.3 % sequence similarity) and to other members of the genusShewanella(91.0–94.9 %). The phenotypic characteristics and DNA–DNA hybridization relatedness data indicate that strain DW01Tshould be distinguished fromS. algaeATCC 51192T. On the basis of the data presented in this study, strain DW01Trepresents a novel species, for which the nameShewanella haliotissp. nov. is proposed. The type strain is DW01T(=KCTC 12896T=JCM 14758T).
Methylobacterium platani sp. nov., isolated from a leaf of the tree Platanus orientalis
Authors: Kang Yoon-Suk , Kim Juhyun , Shin Hyeon-Dong , Nam Young-Do , Bae Jin-Woo , Jeon Che Ok , Park Woojun
Published: November 2007

A novel bacterial strain, designated PMB02T, was isolated from a leaf of the treePlatanus orientalis. Colonies grown on TYG agar plates were circular, pink-pigmented and slow-growing, being 0.2–1.5 mm in diameter after 3 days growth. The cells of strain PMB02Twere Gram-negative, aerobic, motile rods that possessed oxidase and catalase activities and grew at 20–30 °C, pH 6–8 and in media containing less than 1 % NaCl. The major respiratory quinone was identified as Q-10. A phylogenetic analysis based on 16S rRNA gene sequence comparisons indicated that strain PMB02Twas related to members of the genusMethylobacterium. A comparative 16S rRNA gene sequence-based phylogenetic analysis placed the strain in a clade with the speciesMethylobacterium aquaticumandMethylobacterium variabile, with which it showed sequence similarities of 97.7 and 97.4 %, respectively. The values for DNA–DNA hybridization between strain PMB02TandM. aquaticumCCM 7218TandM. variabileGR3Twere less than 32 %. On the basis of the phenotypic characterization, the phylogenetic analysis and the DNA–DNA relatedness data, strain PMB02Tis considered to represent a novel species of the genusMethylobacterium, for which the nameMethylobacterium platanisp. nov. is proposed. The type strain is PMB02T(=KCTC 12901T=JCM 14648T).
Prevotella maculosa sp. nov., isolated from the human oral cavity
Authors: Downes Julia , Sutcliffe Iain C. , Booth Veronica , Wade William G.
Published: November 2007

Three strains of anaerobic Gram-negative bacilli isolated from human oral sites were subjected to a comprehensive range of phenotypic and genotypic tests and were found to comprise a homogeneous group. 16S rRNA gene sequence analysis revealed the strains to constitute a novel group within the genus Prevotella, most closely related to Prevotella oris and Prevotella salivae. A novel species, Prevotella maculosa sp. nov., is proposed to accommodate these strains. Prevotella maculosa is saccharolytic and produces acetic and succinic acids as end products of fermentation. The G+C content of the DNA of the type strain is 48 mol%. The type strain of Prevotella maculosa is W1609T (=DSM 19339T =CCUG 54766T).