bluuebunny/crossref_metadata_2025 huggingface dataset:
A structure-based mechanism for benzalacetone synthase from
Rheum palmatum
Authors: Morita Hiroyuki , Shimokawa Yoshihiko , Tanio Michikazu , Kato Ryohei , Noguchi Hiroshi , Sugio Shigetoshi , Kohno Toshiyuki , Abe Ikuro
Published: December 2009

Benzalacetone synthase (BAS), a plant-specific type III polyketide synthase (PKS), catalyzes a one-step decarboxylative condensation of malonyl-CoA and 4-coumaroyl-CoA to produce the diketide benzalacetone. We solved the crystal structures of both the wild-type and chalcone-producing I207L/L208F mutant of
Rheum palmatum
BAS at 1.8 Å resolution. In addition, we solved the crystal structure of the wild-type enzyme, in which a monoketide coumarate intermediate is covalently bound to the catalytic cysteine residue, at 1.6 Å resolution. This is the first direct evidence that type III PKS utilizes the cysteine as the nucleophile and as the attachment site for the polyketide intermediate. The crystal structures revealed that BAS utilizes an alternative, novel active-site pocket for locking the aromatic moiety of the coumarate, instead of the chalcone synthase’s coumaroyl-binding pocket, which is lost in the active-site of the wild-type enzyme and restored in the I207L/L208F mutant. Furthermore, the crystal structures indicated the presence of a putative nucleophilic water molecule which forms hydrogen bond networks with the Cys-His-Asn catalytic triad. This suggested that BAS employs novel catalytic machinery for the thioester bond cleavage of the enzyme-bound diketide intermediate and the final decarboxylation reaction to produce benzalacetone. These findings provided a structural basis for the functional diversity of the type III PKS enzymes.
Consensus motif for integrin transmembrane helix association
Authors: Berger Bryan W. , Kulp Daniel W. , Span Lisa M. , DeGrado Jessica L. , Billings Paul C. , Senes Alessandro , Bennett Joel S. , DeGrado William F.
Published: December 2009

Interactions between transmembrane (TM) helices play an important role in the regulation of diverse biological functions. For example, the TM helices of integrins are believed to interact heteromerically in the resting state; disruption of this interaction results in integrin activation and cellular adhesion. However, it has been difficult to demonstrate the specificity and affinity of the interaction between integrin TM helices and to relate them to the activation process. To examine integrin TM helix associations, we developed a bacterial reporter system and used it to define the sequence motif required for helix–helix interactions in the
β
1
and
β
3
integrin subfamilies. The helices interact in a novel three-dimensional motif, the “reciprocating large-small motif” that is also observed in the crystal structures of unrelated proteins. Modest but specific stabilization of helix associations is realized via packing of complementary small and large groups on neighboring helices. Mutations destabilizing this motif activate native, full-length integrins. Thus, this highly conserved dissociable motif plays a vital and widespread role as an on-off switch that can integrate with other control elements during integrin activation.
Template-dependent 3
′
–5
′
nucleotide addition is a shared feature of tRNA
His
guanylyltransferase enzymes from multiple domains of life
Authors: Abad Maria G. , Rao Bhalchandra S. , Jackman Jane E.
Published: December 2009

The presence of an additional 5
′
guanosine residue (G
-1
) is a unique feature of tRNA
His
. G
-1
is incorporated posttranscriptionally in eukarya via an unusual 3
′
–5
′
nucleotide addition reaction catalyzed by the tRNA
His
guanylyltransferase (Thg1). Yeast Thg1 catalyzes an unexpected second activity: Watson–Crick-dependent 3
′
–5
′
nucleotide addition that occurs in the opposite direction to nucleotide addition by all known DNA and RNA polymerases. This discovery led to the hypothesis that there are alternative roles for Thg1 family members that take advantage of this unusual enzymatic activity. Here we show that archaeal homologs of Thg1 catalyze G
-1
addition, in vitro and in vivo in yeast, but only in a templated reaction, i.e. with tRNA
His
substrates that contain a C
73
discriminator nucleotide. Because tRNA
His
from archaea contains C
73
, these findings are consistent with a physiological function for templated nucleotide addition in archaeal tRNA
His
maturation. Moreover, unlike yeast Thg1, archaeal Thg1 enzymes also exhibit a preference for template-dependent U
-1
addition to A
73
-containing tRNA
His
. Taken together, these results demonstrate that Watson–Crick template-dependent 3
′
–5
′
nucleotide addition is a shared catalytic activity exhibited by Thg1 family members from multiple domains of life, and therefore, that this unusual reaction may constitute an ancestral activity present in the earliest members of the Thg1 enzyme family.
Excitatory neurons of the proprioceptive, interoceptive, and arousal hindbrain networks share a developmental requirement for
Math1
Authors: Rose Matthew F. , Ahmad Kaashif A. , Thaller Christina , Zoghbi Huda Y.
Published: December 2009

Hindbrain networks important for sensation and arousal contain diverse neuronal populations with distinct projections, yet share specific characteristics such as neurotransmitter expression. The relationship between the function of these neurons, their developmental origin, and the timing of their migration remains unclear. Mice lacking the proneural transcription factor
Math1
(
Atoh1
) lose neurons essential for hearing, balance, and unconscious proprioception. By using a new, inducible
Math1

Cre
*
PR

allele, we found that
Math1
is also required for the conscious proprioceptive system, including excitatory projection neurons of the dorsal column nuclei and for vital components of the interoceptive system, such as Barrington's nucleus, that is closely associated with arousal. In addition to specific networks,
Math1
lineages shared specific neurotransmitter expression, including glutamate, acetylcholine, somatostatin, corticotropin releasing hormone, and nitric oxide. These findings identify twenty novel
Math1
lineages and indicate that the
Math1
network functions partly as an interface for conscious (early-born) and unconscious (late-born) proprioceptive inputs to the cortex and cerebellum, respectively. In addition, these data provide previously unsuspected genetic and developmental links between proprioception, interoception, hearing, and arousal.
Swimming bacteria power microscopic gears
Authors: Sokolov Andrey , Apodaca Mario M. , Grzybowski Bartosz A. , Aranson Igor S.
Published: December 2009

Whereas the laws of thermodynamics prohibit extraction of useful work from the Brownian motion of particles in equilibrium, these motions can be “rectified” under nonequilibrium conditions, for example, in the presence of asymmetric geometrical obstacles. Here, we describe a class of systems in which aerobic bacteria
Bacillus subtilis
moving randomly in a fluid film power submillimeter gears and primitive systems of gears decorated with asymmetric teeth. The directional rotation is observed only in the regime of collective bacterial swimming and the gears’ angular velocities depend on and can be controlled by the amount of oxygen available to the bacteria. The ability to harness and control the power of collective motions appears an important requirement for further development of mechanical systems driven by microorganisms.
webMGR: an online tool for the multiple genome rearrangement problem
Authors: Lin Chi Ho , Zhao Hao , Lowcay Sean Harry , Shahab Atif , Bourque Guillaume
Published: December 2009

Summary: The algorithm MGR enables the reconstruction of rearrangement phylogenies based on gene or synteny block order in multiple genomes. Although MGR has been successfully applied to study the evolution of different sets of species, its utilization has been hampered by the prohibitive running time for some applications. In the current work, we have designed new heuristics that significantly speed up the tool without compromising its accuracy. Moreover, we have developed a web server (webMGR) that includes elaborate web output to facilitate navigation through the results.

Availability: webMGR can be accessed via http://www.gis.a-star.edu.sg/~bourque. The source code of the improved standalone version of MGR is also freely available from the web site.

Contact:  bourque@gis.a-star.edu.sg

Supplementary information:  Supplementary data are available at Bioinformatics online.
Copy number variant detection in inbred strains from short read sequence data
Authors: Simpson Jared T. , McIntyre Rebecca E. , Adams David J. , Durbin Richard
Published: December 2009

Summary: We have developed an algorithm to detect copy number variants (CNVs) in homozygous organisms, such as inbred laboratory strains of mice, from short read sequence data. Our novel approach exploits the fact that inbred mice are homozygous at virtually every position in the genome to detect CNVs using a hidden Markov model (HMM). This HMM uses both the density of sequence reads mapped to the genome, and the rate of apparent heterozygous single nucleotide polymorphisms, to determine genomic copy number. We tested our algorithm on short read sequence data generated from re-sequencing chromosome 17 of the mouse strains A/J and CAST/EiJ with the Illumina platform. In total, we identified 118 copy number variants (43 for A/J and 75 for CAST/EiJ). We investigated the performance of our algorithm through comparison to CNVs previously identified by array-comparative genomic hybridization (array CGH). We performed quantitative-PCR validation on a subset of the calls that differed from the array CGH data sets.

Availability: The software described in this manuscript, named cnD for copy number detector, is free and released under the GPL. The program is implemented in the D programming language using the Tango library. Source code and pre-compiled binaries are available at http://www.sanger.ac.uk/resources/software/cnd.html

Contact:  rd@sanger.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Biocharts: a visual formalism for complex biological systems
Authors: Kugler Hillel , Larjo Antti , Harel David
Published: December 2009

We address one of the central issues in devising languages, methods and tools for the modelling and analysis of complex biological systems, that of linking high-level (e.g. intercellular) information with lower-level (e.g. intracellular) information. Adequate ways of dealing with this issue are crucial for understanding biological networks and pathways, which typically contain huge amounts of data that continue to grow as our knowledge and understanding of a system increases. Trying to comprehend such data using the standard methods currently in use is often virtually impossible. We propose a two-tier compound visual language, which we call
Biocharts
, that is geared towards building fully executable models of biological systems. One of the main goals of our approach is to enable biologists to actively participate in the computational modelling effort, in a natural way. The high-level part of our language is a version of statecharts, which have been shown to be extremely successful in software and systems engineering. The statecharts can be combined with any appropriately well-defined language (preferably a diagrammatic one) for specifying the low-level dynamics of the pathways and networks. We illustrate the language and our general modelling approach using the well-studied process of bacterial chemotaxis.
How necessary is a fast testkit for mitigation of pandemic flu?
Authors: Chin Juxin , Koh Geoffrey , Lee Dong-Yup
Published: December 2009

It is widely feared that a novel, highly pathogenic, human transmissible influenza virus may evolve that could cause the next global pandemic. Mitigating the spread of such an influenza pandemic would require not only the timely administration of antiviral drugs to those infected, but also the implementation of suitable intervention policies for stunting the spread of the virus. Towards this end, mathematical modelling and simulation studies are crucial as they allow us to evaluate the predicted effectiveness of the various intervention policies before enforcing them. Diagnosis plays a vital role in the overall pandemic management framework by detecting and distinguishing the pathogenic strain from the less threatening seasonal strains and other influenza-like illnesses. This allows treatment and intervention to be deployed effectively, given limited antiviral supplies and other resources. However, the time required to design a fast and accurate testkit for novel strains may limit the role of diagnosis. Herein, we aim to investigate the cost and effectiveness of different diagnostic methods using a stochastic agent-based city-scale model, and then address the issue of whether conventional testing approaches, when used with appropriate intervention policies, can be as effective as fast testkits in containing a pandemic outbreak. We found that for mitigation purposes, fast and accurate testkits are not necessary as long as sufficient medication is given, and are generally recommended only when used with extensive contact tracing and prophylaxis. Additionally, in the event of insufficient medication and fast testkits, the use of slower, conventional testkits together with proper isolation policies while waiting for the diagnostic results can be an equally effective substitute.
Photobacterium gaetbulicola sp. nov., a lipolytic bacterium isolated from a tidal flat sediment
Authors: Kim Young-Ok , Kim Kyung-Kil , Park Sooyeon , Kang So-Jung , Lee Jeong-Ho , Lee Sang-Jun , Oh Tae-Kwang , Yoon Jung-Hoon
Published: December 2009

A Gram-negative, motile, non-spore-forming and lipolytic bacterial strain, designated Gung47T, was isolated from a tidal flat on the west coast of Korea. Strain Gung47T grew optimally at 30 °C and with 2−5 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain Gung47T belonged to the genus Photobacterium. Strain Gung47T exhibited 98.1 % 16S rRNA gene sequence similarity with Photobacterium rosenbergii LMG 22223T and 94.3–96.3 % similarity with other type strains of species of the genus Photobacterium. Strain Gung47T exhibited 47 % DNA–DNA relatedness to P. rosenbergii LMG 22223T. Strain Gung47T contained Q-8 as the predominant ubiquinone and C16 : 1
ω7c and/or iso-C15 : 0 2-OH, C16 : 0 and C18 : 1
ω7c as the major fatty acids. In this study, two closely related type strains, P. rosenbergii LMG 22223T and Photobacterium
halotolerans LMG 22194T, were also found to have Q-8 as the predominant ubiquinone. The DNA G+C content of strain Gung47T was 50.6 mol%. The differential phenotypic properties together with the phylogenetic and genetic distinctiveness of strain Gung47T demonstrated that this strain is distinguishable from recognized Photobacterium species. Therefore, strain Gung47T is considered to represent a novel species of the genus Photobacterium, for which the name Photobacterium gaetbulicola sp. nov. is proposed. The type strain is Gung47T (=KCTC 22804T =CCUG 58399T).
Genomic Inventory and Transcriptional Analysis of Medicago truncatula Transporters
Authors: Benedito Vagner A. , Li Haiquan , Dai Xinbin , Wandrey Maren , He Ji , Kaundal Rakesh , Torres-Jerez Ivone , Gomez S. Karen , Harrison Maria J. , Tang Yuhong , Zhao Patrick X. , Udvardi Michael K.
Published: December 2009

Transporters move hydrophilic substrates across hydrophobic biological membranes and play key roles in plant nutrition, metabolism, and signaling and, consequently, in plant growth, development, and responses to the environment. To initiate and support systematic characterization of transporters in the model legume Medicago truncatula, we identified 3,830 transporters and classified 2,673 of these into 113 families and 146 subfamilies. Analysis of gene expression data for 2,611 of these transporters identified 129 that are expressed in an organ-specific manner, including 50 that are nodule specific and 36 specific to mycorrhizal roots. Further analysis uncovered 196 transporters that are induced at least 5-fold during nodule development and 44 in roots during arbuscular mycorrhizal symbiosis. Among the nodule- and mycorrhiza-induced transporter genes are many candidates for known transport activities in these beneficial symbioses. The data presented here are a unique resource for the selection and functional characterization of legume transporters.
The Involvement of Lipid Peroxide-Derived Aldehydes in Aluminum Toxicity of Tobacco Roots
Authors: Yin Lina , Mano Jun'ichi , Wang Shiwen , Tsuji Wataru , Tanaka Kiyoshi
Published: December 2009

Oxidative injury of the root elongation zone is a primary event in aluminum (Al) toxicity in plants, but the injuring species remain unidentified. We verified the hypothesis that lipid peroxide-derived aldehydes, especially highly electrophilic α,β-unsaturated aldehydes (2-alkenals), participate in Al toxicity. Transgenic tobacco (Nicotiana tabacum) overexpressing Arabidopsis (Arabidopsis thaliana) 2-alkenal reductase (AER-OE plants), wild-type SR1, and an empty vector-transformed control line (SR-Vec) were exposed to AlCl3 on their roots. Compared with the two controls, AER-OE plants suffered less retardation of root elongation under AlCl3 treatment and showed more rapid regrowth of roots upon Al removal. Under AlCl3 treatment, the roots of AER-OE plants accumulated Al and H2O2 to the same levels as did the sensitive controls, while they accumulated lower levels of aldehydes and suffered less cell death than SR1 and SR-Vec roots. In SR1 roots, AlCl3 treatment markedly increased the contents of the highly reactive 2-alkenals acrolein, 4-hydroxy-(E)-2-hexenal, and 4-hydroxy-(E)-2-nonenal and other aldehydes such as malondialdehyde and formaldehyde. In AER-OE roots, accumulation of these aldehydes was significantly less. Growth of the roots exposed to 4-hydroxy-(E)-2-nonenal and (E)-2-hexenal were retarded more in SR1 than in AER-OE plants. Thus, the lipid peroxide-derived aldehydes, formed downstream of reactive oxygen species, injured root cells directly. Their suppression by AER provides a new defense mechanism against Al toxicity.
Time pressure, task complexity, and audit effectiveness
Authors: Bowrin Anthony R. , King James
Published: December 2009

Purpose

The purpose of this paper is to examine the relationships among time pressure (TP), task complexity (TC), and audit effectiveness (AE). It is motivated by the conflicting results reported in prior TP studies.

Design/methodology/approach

The research hypotheses are developed using McGrath's interactional model of the Yerkes‐Dodson Law. Data are collected using a two‐treatment field experiment involving 63 public accountants.

Findings

The results show a negative, interactional relationship among TP, TC, and AE.

Research limitations/implications

The first limitation concerns the non‐random procedure used to recruit public accounting firms and auditors. Second, there is the less than perfect operationalization of the TC construct.

Practical implications

First, the findings suggest that public accounting firms may need to resist the urge to reduce the time allowed for performing compliance tests, and provide training to improve the detection rate for all type of compliance deviations. Second, the fact that the rate of change in AE, in response to changes in TP, is different for the two audit tasks studied, suggests that it may not be appropriate for audit planners to assume a uniform TP effect across the various tasks involved in an audit. This insight has implication for the trade‐offs between the lower direct audit costs associated with tighter time budgets, and possible increases in audit risk associated with lower AE.

Originality/value

Two unique aspects of this paper are the operationalization of TP as a continuous random variable and the use of z‐scores to standardize the AE measure.
Risks in the labor market and social insurance preferences: Germany and the USA
Authors: Duman Anil
Published: December 2009

Purpose

The purpose of this paper is to attempt to look at the link between labor market risks and social insurance demands by taking occupational unemployment rates, and specificity of skills into account.

Design/methodology/approach

Occupational unemployment rate is treated as an estimate of labor market risk in addition to human capital investment. Then, the variations in Germany and the USA – with diverse labor markets and a considerable difference in terms of social insurance support – are examined.

Findings

The results suggest that occupational unemployment rate is explanatory for the demands for social insurance along with income.

Practical implications

Conclusions reached in the paper aim to contribute to the understanding of the political support for social insurance and hence provide tools for the design of such insurance mechanisms.

Originality/value

Contrary to the widespread association between the type of human capital and social insurance preferences in the literature, the paper argues that the cross‐country variations can be explained by occupational unemployment rates.
Synthesis and characterisation of low‐cost cardanol polyurethanes
Authors: Athawale Vilas , Shetty Narendra
Published: December 2009

Purpose

The purpose of this paper is to develop a flexible, as well as a rigid, polyurethane (PU) product using polyols derived from renewable resource for suitable application.

Design/methodology/approach

Cardanol is converted into corresponding glycidyl ether by reacting it with epichlorohydrin. The resulting glycidyl ether is hydrolysed to the corresponding diol in the presence of a heteropolyacid, which acted as a catalyst. The diol obtained is used for synthesising PU's by reacting it with various mole ratios of toluene diisocyanate (TDI) and isophorone diisocyanate (IPDI) and their physicomechanical, chemical and morphological properties are studied.

Findings

The polyol selected for the present paper has unique structural characteristics such as C15 chain length, which contributes to flexibility, and an aromatic ring, which imparts rigidity in the final application of resulting PU. By choosing optimum ratio of NCO/OH, it is possible to obtain a system, which can be used for the development of a flexible as well as a rigid polymer for suitable application.

Research limitations/implications

The cardanol and dodecatungstosilic acid used are of a particular grade and of a particular manufacturer. Furthermore, it could be obtained from different sources and of different grades. The spectral studies done are purely qualitative. Gloss is tested for the samples at 600, whereas other angles can also be used.

Practical implications

The method developed provided a simple and practical solution to improve performance characteristics of PU resins, which also proves to be cost effective.

Originality/value

The PU product developed due to its enhanced coating properties can be used in various surface‐coating applications.
Preparation and surface property of core‐shell particles containing fluorinated polymer in shell
Authors: Qin Zonggen , Tu Weiping
Published: December 2009

Purpose

The purpose of this paper is to modify the surface property of polyacrylate latex films using only small amounts of fluorinated acrylate and to optimise the results of such a modification.

Design/methodology/approach

The core‐shell particles with polyacrylate rich in core and containing fluorinated polymer rich in shell are prepared by a two‐stage semi‐continuous emulsion polymerisation under kinetically controlled conditions. The surface properties of the latex films produced from the core‐shell particles are investigated by optical goniometer measurement as well as contact angle method.

Findings

The latex films produced from the core‐shell particles exhibited surface energy of around 10 mN/m. The angle resolved X‐ray photoelectron spectrum measurements showed an increased average fluorine concentration in a surface layer thickness of a few nanometres, when compared to the fluorine concentration in the bulk.

Research limitations/implications

Methyl methacrylate, butyl acrylate and N‐methylol acrylamide monomers are used as co‐monomer to form the shell with fluoroalkyl methacrylate. By preparing core‐shell emulsion with a fluoropolymer in the shell phase, the surface property of polyacrylate latex films is efficiently modified by using only small amounts of fluorinated acrylate monomer.

Practical implications

The method developed provided a simple and practical solution to improving the surface property of polyacrylate latex films.

Originality/value

The method for enhancing surface property of polyacrylate latex films is novel and can find numerous applications in surface coating.
The smarter supply chain of the future
Authors: Butner Karen
Published: December 2009

Purpose

The aims of this paper is to show how supply chains can become a lot smarter to deal effectively with risk and meet business objectives.

Design/methodology/approach

For this Global Chief Supply Chain Officer Study, IBM group leaders interviewed 400 senior executives from North America, Western Europe, and the Asia Pacific region who are responsible for their organizations' supply‐chain strategies and operations.

Findings

Findings in five key areas summarize the state of supply‐chain management today: cost containment; visibility, risk; customer intimacy; and globalization.

Practical implications

IBM sees a different kind of supply chain emerging – a smarter supply chain with three core characteristics: Instrumented – supply‐chain data previously created by people will increasingly be generated by sensors, RFID tags, meters, actuators, GPSs, and other devices and systems; Interconnected – smarter supply chains would take advantage of unprecedented levels of interaction that will facilitate collaboration on a massive scale; and Intelligent – to assist executives in evaluating trade‐offs, intelligent systems will assess myriad constraints and alternatives, allowing decision makers to simulate various courses of action.

Originality/value

Smarter supply chains would have the analytic capability to evaluate myriad alternatives in terms of supply, manufacturing, and distribution – and the flexibility to reconfigure flows as conditions change. Executives could then plan for contingencies and execute them.
The sharing imperative
Authors: Chakravarthy Bala
Published: December 2009

Purpose

This paper aims to explain how undue emphasis on unit accountability can foster parochial behaviors and silo thinking that drive out inter‐unit cooperation. It also aims to warn that growth strategies depend on cross business sharing.

Design/methodology/approach

The author, Royal Dutch Shell Chair Professor of Sustainable Business Growth at IMD, details four steps senior executives can take to fight the growing insularity among a firm's businesses and promote better sharing among them.

Findings

The four steps are: reinforce the company's shared purpose and values; nurture boundary spanners; provide score cards that are balanced between horizontal contributions and vertical contributions; and support the informal organization by encouraging interactions, such as social events.

Practical implications

By nurturing the informal organization, managers encourage a culture of sharing. Sharing between two business units is helped if at least one of them has a boundary spanner who can act as the bridge.

Originality/value

Paradoxically, the very features of a competence that make it distinctive and hard for competitors to procure or copy are also the ones that are more tacit and difficult to share internally as well.
Novel chemoembolization using calcium‐phosphate ceramic microsphere incorporating TNP‐470, an anti‐angiogenic agent
Authors: Emoto Makoto , Naganuma Yasuko , Choijamts Batsuren , Ohno Toshiki , Yoshihisa Hajime , Kanomata Nobuhiko , Kawarabayashi Tatsuhiko , Aizawa Mamoru
Published: December 2009

The purpose of the present study was to develop a new method of chemoembolization to improve the therapeutic effectiveness and safety profile of cancer treatment. A chemoembolization approach was designed for human solid tumors using resorbable calcium‐phosphate ceramic microspheres loaded with an agent anti‐angiogenic to tumor vasculature in vivo. The human uterine sarcoma cell line FU‐MMT‐3 was used in this study because this tumor is aggressive and also exhibits a poor response to radiotherapy or any chemotherapy currently used. The calcium‐phosphate ceramic microspheres loaded with TNP‐470, an anti‐angiogenic agent, were injected into FU‐MMT‐3 xenografts in nude mice three times per week for 8 weeks. The treatment using TNP‐470‐loaded microspheres suppressed tumor growth, compared to treatment with TNP‐470 alone, microspheres alone, and the control. The mean tumor weight after treatment using TNP‐470‐loaded microspheres was significantly lower than that after treatment with microspheres alone. These ceramic microspheres were remarkably embolized in tumor microvessels as well as in the feeding arteries and a significant reduction of intratumoral vascularity was also demonstrated following treatment with TNP‐470‐loaded microspheres. Severe loss of body weight was not observed in any mice treated with the TNP‐470‐loaded microspheres, compared to treatment with TNP‐470 alone. These results suggest that targeting tumor vasculature in human uterine sarcoma using calcium‐phosphate microspheres might be more effective and safer than the treatment that employs anti‐angiogenic agent alone. This new chemoembolization method incorporating an anti‐angiogenic agent may contribute to the effective treatment of locally advanced or recurrent solid tumors.

(Cancer Sci 2010; 101: 984–990)
Primary synovial sarcoma arising from a crossed ectopic kidney with fusion
Authors: Kageyama Susumu , Tsuru Teruhiko , Okamoto Keisei , Narita Mitsuhiro , Okada Yusaku
Published: December 2009

Abstract:  Crossed renal ectopia with fusion is a rare anomaly of the kidney. The present case report describes a 67‐year‐old man with renal tumor who had been diagnosed as having a crossed ectopic kidney with fusion for 25 years. The pathological diagnosis of the primary tumor specimen was Wilms' tumor with favorable histology. Upon tumor recurrence, molecular detection of SYT‐SSX2 fusion transcripts lead to the diagnosis of synovial sarcoma of the kidney. To our knowledge, this is the first case of primary synovial sarcoma arising from a crossed ectopic kidney with fusion.
Transport and Distribution ofSalmonella entericaSerovar Typhimurium in Loamy and Sandy Soil Monoliths with Applied Liquid Manure
Authors: Bech Tina B. , Johnsen Kaare , Dalsgaard Anders , Laegdsmand Mette , Jacobsen Ole Hørbye , Jacobsen Carsten S.
Published: December 2009

A leaching experiment, where liquid manure spiked withSalmonella entericaserovar Typhimurium (Tet+) DSM554 was applied to soil surfaces, was conducted on intact soil monoliths (60 cm in diameter and 100 cm long). A total of 6.5 × 1010CFU was applied to each column. We found thatSalmonellaserovar Typhimurium could be transported to a 1-m depth in loamy soil at concentrations reaching 1.3 × 105CFU/ml of leachate. The test strain was found in concentrations ranging from 300 to 1.35cells/ml in loamy soil throughout the 27 days of the experiment, while concentrations below 20 cells/ml were sporadically detected in the leachates from sandy monoliths. Real-time PCR targetinginvADNA showed a clear correspondence between the total and culturable numbers of cells in the leachate, indicating that most cells leached were viable. On day 28, distribution ofSalmonellaserovar Typhimurium at five depths in the four monoliths was determined. The highest recovery rate, ranging from 1.5% to 3.8% of the total applied inoculum, was found in the top 0.2 m.
Direct-Imaging-Based Quantification of
Bacillus cereus
ATCC 14579 Population Heterogeneity at a Low Incubation Temperature
Authors: den Besten Heidy M. W. , Garcia Diego , Moezelaar Roy , Zwietering Marcel H. , Abee Tjakko
Published: December 2009

Bacillus cereus
ATCC 14579 was cultured in microcolonies on Anopore strips near its minimum growth temperature to directly image and quantify its population heterogeneity at an abusive refrigeration temperature. Eleven percent of the microcolonies failed to grow during low-temperature incubation, and this cold-induced population heterogeneity could be partly attributed to the loss of membrane integrity of individual cells.
High Heterogeneity within Methicillin-Resistant
Staphylococcus aureus
ST398 Isolates, Defined by Cfr9I Macrorestriction-Pulsed-Field Gel Electrophoresis Profiles and
spa
and SCC
mec
Types
Authors: Argudín M. A. , Fetsch A. , Tenhagen B.-A. , Hammerl J. A. , Hertwig S. , Kowall J. , Rodicio M. R. , Käsbohrer A. , Helmuth R. , Schroeter A. , Mendoza M. C. , Bräunig J. , Appel B. , Guerra B.
Published: December 2009

During recent years, the animal-associated methicillin-resistant
Staphylococcus aureus
clone ST398 has extensively been studied. The DNA of these isolates turned out to be refractory to SmaI restriction, and consequently, SmaI is unsuitable for subtyping this clone by standard pulsed-field gel electrophoresis (PFGE). Very recently, ST398 DNA was shown to be digested by Cfr9I, a neoschizomer of SmaI. In the present study, we employed Cfr9I PFGE on 100 German and 5 Dutch ST398 isolates and compared their PFGE profiles, protein A gene variable repeat regions (
spa
types), and types of the staphylococcal cassette chromosome
mec
(SCC
mec
). The isolates (from healthy carrier pigs, clinical samples from pigs, dust from farms, milk, and meat) were assigned to 35 profiles, which were correlated to the SCC
mec
type. A dendrogram with the Cfr9I patterns assigned all profiles to two clusters. Cluster A grouped nearly all isolates with SCC
mec
type V, and cluster B comprised all SCC
mec
type IVa and V* (a type V variant first identified as III) carriers plus one isolate with SCC
mec
type V. Both clusters also grouped methicillin-susceptible
S. aureus
isolates. The association of the majority of isolates with SCC
mec
type V in one large cluster indicated the presence of a successful subclone within the clonal complex CC398 from pigs, which has diversified. In general, the combination of Cfr9I PFGE with
spa
and SCC
mec
typing demonstrated the heterogeneity of the series analyzed and can be further used for outbreak investigations and traceability studies of the MRSA ST398 emerging clone.
Composition of the Landfill Microbial Community as Determined by Application of Domain- and Group-Specific 16S and 18S rRNA-Targeted Oligonucleotide Probes
Authors: McDonald James E. , Allison Heather E. , McCarthy Alan J.
Published: December 2009

The microbial community composition of colonized cotton and leachate samples from a landfill was quantified using small subunit (SSU) rRNA probes (quantitative rRNA hybridization). Relative quantification of bacteria, eukaryotes, and archaea revealed variations in the landfill microbial community between samples from different areas of the landfill site and indicated the presence of potentially novel archaea. Anaerobic fungi were quantified in rumen fluid samples but were not sufficiently abundant for direct detection in the landfill samples.
Caldicellulosiruptor obsidiansis
sp. nov., an Anaerobic, Extremely Thermophilic, Cellulolytic Bacterium Isolated from Obsidian Pool, Yellowstone National Park
Authors: Hamilton-Brehm Scott D. , Mosher Jennifer J. , Vishnivetskaya Tatiana , Podar Mircea , Carroll Sue , Allman Steve , Phelps Tommy J. , Keller Martin , Elkins James G.
Published: December 2009

A novel, obligately anaerobic, extremely thermophilic, cellulolytic bacterium, designated OB47
T
, was isolated from Obsidian Pool, Yellowstone National Park, WY. The isolate was a nonmotile, non-spore-forming, Gram-positive rod approximately 2 μm long by 0.2 μm wide and grew at temperatures between 55 and 85°C, with the optimum at 78°C. The pH range for growth was 6.0 to 8.0, with values of near 7.0 being optimal. Growth on cellobiose produced the fastest specific growth rate at 0.75 h
−1
. The organism also displayed fermentative growth on glucose, maltose, arabinose, fructose, starch, lactose, mannose, sucrose, galactose, xylose, arabinogalactan, Avicel, xylan, filter paper, processed cardboard, pectin, dilute acid-pretreated switchgrass, and
Populus
. OB47
T
was unable to grow on mannitol, fucose, lignin, Gelrite, acetate, glycerol, ribose, sorbitol, carboxymethylcellulose, and casein. Yeast extract stimulated growth, and thiosulfate, sulfate, nitrate, and sulfur were not reduced. Fermentation end products were mainly acetate, H
2
, and CO
2
, although lactate and ethanol were produced in 5-liter batch fermentations. The G+C content of the DNA was 35 mol%, and sequence analysis of the small subunit rRNA gene placed OB47
T
within the genus
Caldicellulosiruptor
. Based on its phylogenetic and phenotypic properties, the isolate is proposed to be designated
Caldicellulosiruptor obsidiansis
sp. nov. and OB47 is the type strain (ATCC BAA-2073).
Critical Evaluation of the Volumetric “Bottle Effect” on Microbial Batch Growth
Authors: Hammes Frederik , Vital Marius , Egli Thomas
Published: December 2009

We have analyzed the impact of surface-to-volume ratio on final bacterial concentrations after batch growth. We examined six bottle sizes (20 to 1,000 ml) using three independent enumeration methods to quantify growth. We found no evidence of a so-called volumetric bottle effect, thus contradicting numerous previous reports.
Indirect Effects of Temperature on Stink Bug Fitness, via Maintenance of Gut-Associated Symbionts
Authors: Prado Simone S. , Hung Kim Y. , Daugherty Matthew P. , Almeida Rodrigo P. P.
Published: December 2009

Impacts of climate change on organisms are already apparent, with effects ranging from the individual to ecosystem scales. For organisms engaged in mutualisms, climate may affect population performance directly or indirectly through mediated effects on their mutualists. We tested this hypothesis for two stink bugs,
Acrosternum hilare
and
Murgantia histrionica
, and their gut-associated symbionts. We reared these species at two constant temperatures, 25 and 30°C, and monitored population demographic parameters and the presence of gut-associated symbionts with diagnostic PCR primer sets. Both stink bugs lost their respective gut symbionts within two generations at 30°C. In addition, the insect survivorship and reproductive rates of both
A. hilare
and
M. histrionica
at 30°C were lower than at 25°C. Other demographic parameters also indicated a decrease in overall insect fitness at the high temperature. Collectively our data showed that the decrease in host fitness was coupled with, and potentially mediated by, symbiont loss at 30°C. This work illustrates the need to better understand the biology of animal-symbiont associations and the consequences of local climate for the dynamics of these interactions.
Metabolic Impact of Increased NADH Availability in
Saccharomyces cerevisiae
Authors: Hou Jin , Scalcinati Gionata , Oldiges Marco , Vemuri Goutham N.
Published: December 2009

Engineering the level of metabolic cofactors to manipulate metabolic flux is emerging as an attractive strategy for bioprocess applications. We present the metabolic consequences of increasing NADH in the cytosol and the mitochondria of
Saccharomyces cerevisiae
. In a strain that was disabled in formate metabolism, we either overexpressed the native NAD
+
-dependent formate dehydrogenase in the cytosol or directed it into the mitochondria by fusing it with the mitochondrial signal sequence encoded by the
CYB2
gene. Upon exposure to formate, the mutant strains readily consumed formate and induced fermentative metabolism even under conditions of glucose derepression. Cytosolic overexpression of formate dehydrogenase resulted in the production of glycerol, while when this enzyme was directed into the mitochondria, we observed glycerol and ethanol production. Clearly, these results point toward different patterns of compartmental regulation of redox homeostasis. When pulsed with formate,
S. cerevisiae
cells growing in a steady state on glucose immediately consumed formate. However, formate consumption ceased after 20 min. Our analysis revealed that metabolites at key branch points of metabolic pathways were affected the most by the genetic perturbations and that the intracellular concentrations of sugar phosphates were specifically affected by time. In conclusion, the results have implications for the design of metabolic networks in yeast for industrial applications.
Effect of Daily Temperature Fluctuation during the Cool Season on the Infectivity ofCryptosporidium parvum
Authors: Li Xunde , Atwill Edward R. , Dunbar Lissa A. , Tate Kenneth W.
Published: December 2009

The present work calculated the rate of inactivation ofCryptosporidium parvumoocysts attributable to daily oscillations of low ambient temperatures. The relationship between air temperature and the internal temperature of bovine feces on commercial operations was measured, and three representative 24-h thermal regimens in the ∼15°C, ∼25°C, and ∼35°C ranges were chosen and emulated using a thermocycler.C. parvumoocysts suspended in deionized water were exposed to the temperature cycles, and their infectivity in mice was tested. Oral inoculation of 103treated oocysts per neonatal BALB/c mouse (∼14 times the 50% infective dose) resulted in time- and temperature-dependent reductions in the proportion of infected mice. Oocysts were completely noninfectious after 14 24-h cycles with the 30°C regimen and after 70 24-h cycles with the 20°C regimen. In contrast, oocysts remained infectious after 90 24-h cycles with the 10°C regimens. The estimated numbers of days needed for a 1-log10reduction inC. parvumoocyst infectivity were 4.9, 28.7, and 71.5 days for the 30, 20, and 10°C thermal regimens, respectively. The loss of infectivity of oocysts induced by these thermal regimens was due in part to partial or completein vitroexcystation.
Physical Characteristics of Spores of Food-Associated Isolates of the
Bacillus cereus
Group
Authors: Ankolekar Chandrakant , Labbé Ronald G.
Published: December 2009

All 47 food-borne isolates of
Bacillus cereus sensu stricto
, as well as 10 of 12 food-borne, enterotoxigenic isolates of
Bacillus thuringiensis
, possessed appendages. Spores were moderately to highly hydrophobic, and each had a net negative charge. These characteristics indicate that spores of food-associated
B. thuringiensis
and not only
B. cereus sensu stricto
have high potential to adhere to inert surfaces.
Studying the Dynamics of Flagella in Multicellular Communities of
Escherichia coli
by Using Biarsenical Dyes
Authors: Copeland Matthew F. , Flickinger Shane T. , Tuson Hannah H. , Weibel Douglas B.
Published: December 2009

This paper describes a new approach for labeling intact flagella using the biarsenical dyes FlAsH and ReAsH and imaging their spatial and temporal dynamics on live
Escherichia coli
cells in swarming communities of bacteria by using epifluorescence microscopy. Using this approach, we observed that (i) bundles of flagella on swarmer cells remain cohesive during frequent collisions with neighboring cells, (ii) flagella on nonmotile swarmer cells at the leading edge of the colony protrude in the direction of the uncolonized agar surface and are actively rotated in a thin layer of fluid that extends outward from the colony, and (iii) flagella form transient interactions with the flagella of other swarmer cells that are in close proximity. This approach opens a window for observing the dynamics of cells in communities that are relevant to ecology, industry, and biomedicine.
Comparison of PCR Binary Typing (P-BIT), a New Approach to Epidemiological Subtyping of
Campylobacter jejuni
, with Serotyping, Pulsed-Field Gel Electrophoresis, and Multilocus Sequence Typing Methods
Authors: Cornelius Angela J. , Gilpin Brent , Carter Philip , Nicol Carolyn , On Stephen L. W.
Published: December 2009

To overcome some of the deficiencies with current molecular typing schema for
Campylobacter
spp., we developed a prototype PCR binary typing (P-BIT) approach. We investigated the distribution of 68 gene targets in 58
Campylobacter jejuni
strains, one
Campylobacter lari
strain, and two
Campylobacter coli
strains for this purpose. Gene targets were selected on the basis of distribution in multiple genomes or plasmids, and known or putative status as an epidemicity factor. Strains were examined with Penner serotyping, pulsed-field gel electrophoresis (PFGE; using SmaI and KpnI enzymes), and multilocus sequence typing (MLST) approaches for comparison. P-BIT provided 100% typeability for strains and gave a diversity index of 98.5%, compared with 97.0% for SmaI PFGE, 99.4% for KpnI PFGE, 96.1% for MLST, and 92.8% for serotyping. Numerical analysis of the P-BIT data clearly distinguished strains of the three
Campylobacter
species examined and correlated somewhat with MLST clonal complex assignations and with previous classifications of “high” and “low” risk. We identified 18 gene targets that conferred the same level of discrimination as the 68 initially examined. We conclude that P-BIT is a useful approach for subtyping, offering advantages of speed, cost, and potential for strain risk ranking unavailable from current molecular typing schema for
Campylobacter
spp.
Transfer of a Phage T4 Gene into
Enterobacteriaceae
, Determined at the Single-Cell Level
Authors: Kenzaka Takehiko , Nasu Masao , Tani Katsuji
Published: December 2009

The transfer range of phage genes was investigated at the single-cell level by using an
in situ
DNA amplification technique. After absorption of phages, a phage T4 gene was maintained in the genomes of non-plaque-forming bacteria at frequencies of 10
−2
gene copies per cell. The gene transfer decreased the mutation frequencies in nonhost recipients.
Inhibitory Effects of Low-Energy Pulsed Ultrasonic Stimulation on Cell Surface Protein Antigen C through Heat Shock Proteins GroEL and DnaK inStreptococcus mutans
Authors: Ishibashi Kazuya , Shimada Koichi , Kawato Takayuki , Kaji Shigejyu , Maeno Masao , Sato Shuichi , Ito Koichi
Published: December 2009

This study concerns the use of low-energy pulsed ultrasound as nondestructive photodynamic antimicrobial therapy for controlling dental plaque. We examined the antibacterial and bactericidal effects of low-energy pulsed ultrasound on mutans streptococci and its inhibitory effects on bacterial cell adhesion ofStreptococcus mutans. The results indicated weak antibacterial and bactericidal effects. However, ultrasonic stimulation for less than 20 min markedly decreased bacterial cell adhesion. To analyze the mechanism underlying the inhibitory effect, we examined cell surface protein antigen C (PAc) and glucosyltransferase I (GTF-I) expression inS. mutans. The levels of PAc gene and protein expression were markedly decreased by ultrasonic stimulation for 20 min. However, no change in GTF-I expression was observed. The expression of stress response heat shock proteins GroEL and DnaK was also examined. GroEL and DnaK levels were significantly decreased by ultrasonic stimulation, and the expression of the PAc protein was also diminished upon the addition of GroEL or DnaK inhibitors without ultrasonic stimulation. These observations suggest that the expression of the PAc protein inS. mutansmay be dependent on heat shock proteins. Thus, low-energy pulsed ultrasound decreases bacterial adhesion by the inhibitory effect on the PAc protein and heat shock protein expression and may be useful as photodynamic antimicrobial chemotherapy in controlling dental plaque.