bluuebunny/crossref_metadata_2025 huggingface dataset:
Short‐Days Induce Weight Loss in Siberian Hamsters Despite Overexpression of the Agouti‐Related Peptide Gene
Authors: Jethwa P. H. , Warner A. , Fowler M. J. , Murphy M. , De Backer M. W. , Adan R. A. H. , Barrett P. , Brameld J. M. , Ebling F. J. P.
Published: March 2010

Many vertebrates express profound annual cycles of body fattening, although it is not clear whether these represent differential activity of the central pathways known to mediate homeostatic control of food intake and energy expenditure, or whether the recent discovery of a major role for pars tuberalis‐ependymal signalling points towards novel mechanisms. We examined this in the Siberian hamster (Phodopus sungorus) by using gene transfection to up‐regulate a major orexigenic peptide, agouti‐related peptide (AgRP), and then determined whether this increased anabolic drive could prevent the short‐day induced winter catabolic state. Infusions of a recombinant adeno‐associated virus encoding an AgRP construct into the hypothalamus of hamsters in the long‐day obese phase of their seasonal cycle produced a 20% gain in body weight over 6 weeks compared to hamsters receiving a control reporter construct, reflecting a significant increase in food intake and a significant decrease in energy expenditure. However, all hamsters showed a significant, prolonged decrease in body weight when exposed to short photoperiods, despite the hamsters expressing the AgRP construct maintaining a higher food intake and lower energy expenditure relative to the control hamsters. Visualisation of the green fluorescent protein reporter and analysis of AgRP‐immunoreactivity confirmed widespread expression of the construct in the hypothalamus, which was maintained for the 21‐week duration of the study. In conclusion, the over‐expression of AgRP in the hypothalamus produced a profoundly obese state but did not block the seasonal catabolic response, suggesting a separation of rheostatic mechanisms in seasonality from those maintaining homeostasis of energy metabolism.
Timing of deep‐sea adaptation in dogfish sharks: insights from a supertree of extinct and extant taxa
Authors: Klug Stefanie , Kriwet Jürgen
Published: March 2010

Klug, S. & Kriwet, J. (2010). Timing of deep‐sea adaptation in dogfish sharks: insights from a supertree of extinct and extant taxa. —Zoologica Scripta, 39, 331–342.

Dogfish sharks (Squaliformes) constitute a monophyletic group of predominantly deep‐water neoselachians, but the reasons and timing of their adaptation to this hostile environment remain ambiguous. Late Cretaceous dogfish sharks, which generally would be associated with deep‐water occur predominantly in shallow water environments. Did the end‐Cretaceous mass extinction event that eliminated large numbers of both terrestrial and aquatic taxa and clades including sharks trigger the evolutionary adaptation of present deep‐water dogfish sharks? Here, we construct, date, and analyse a genus‐level phylogeny of extinct and living dogfish sharks to bring a new perspective to this question. For this, eleven partial source trees of dogfish shark interrelationships were merged to create a comprehensive phylogenetic hypothesis. The resulting supertree is the most inclusive estimate of squaliform interrelationships that has been proposed to date containing 23 fossil and extant members of all major groups. †Eoetmopterus represents the oldest dalatoid. †Microetmopterus, †Paraphorosoides, †Proetmopterus and †Squaliogaleus are stem‐group dalatoids in which bioluminescence most likely was not developed. According to our analyses, bioluminescence in dogfish sharks was already developed in the early Late Cretaceous indicating that these sharks adapted to deep‐water conditions most likely at about 100 Mya. The advantage of this reconstruction is that the fossil record is used directly for age node estimates rather than employing molecular clock approaches.
Distribution and characterization of more than 1000 T‐DNA tags in the genome of Brachypodium distachyon community standard line Bd21
Authors: Thole Vera , Worland Barbara , Wright Jonathan , Bevan Michael W. , Vain Philippe
Published: March 2010

A collection of 4117 fertile T‐DNA lines has been generated by Agrobacterium‐mediated transformation of the diploid community standard line Bd21 of Brachypodium distachyon. The regions flanking the T‐DNA left and right borders of the first 741 transformed plants were isolated by adapter‐ligation PCR and sequenced. A total of 1005 genomic sequences (representing 44.1% of all flanking sequences retrieved) characterized 660 independent T‐DNA loci assigned to a unique location in the Brachypodium genome sequence. Seventy‐six percent of the fertile plant lines contained at least one anchored T‐DNA locus (1.17 loci per tagged line on average). Analysis of the regions flanking both borders of the T‐DNA increased the number of T‐DNA loci tagged and the number of tagged lines by approximately 50% when compared to a single border analysis. T‐DNA integration (2.4 insertions per Mb on average) was proportional to chromosome size, however, varied greatly along each chromosome with often low insertion level around centromeres. The frequency of insertion within transposable elements (5.3%) was fivefold lower than expected if random insertion would have occurred. More than half of the T‐DNAs inserted in genic regions. On average, one gene could be tagged for every second fertile plant line produced and more than one plant line out of three contained a T‐DNA insertion directly within or 500 bp around the coding sequence. Approximately, 60% of the genes tagged corresponded to expressed genes. The T‐DNA lines generated by the BrachyTAG programme are available as a community resource and have been distributed internationally since 2008 via the BrachyTAG.org web site.
Exploring game experiences and game leadership in massively multiplayer online role‐playing games
Authors: Jang YeiBeech , Ryu SeoungHo
Published: March 2010

This study explored the in‐game experiences of massively multiplayer online role‐playing game (MMORPG) players focusing on game leadership and offline leadership. MMORPGs have enormous potential to provide gameplayers with rich social experiences through various interactions along with social activities such as joining a game community, team play and others. In this study, a total of 808 Korean online gameplayers participated in an online survey. Amongst them, 300 MMORPG players were used as the final sample group. The results showed that joining a game community and playing in teams may help players build their leadership experience in games. The findings also suggest that there is a significant positive relationship between in‐game leadership and offline leadership. However, there were no significant differences in gender regarding in‐game and offline leadership. This study suggests that MMORPGs offer a useful place where people can grow their leadership skills and potentially transfer them into the real world.
Management of advanced hepatocellular carcinoma in the era of targeted therapy
Authors: Yau Thomas , Chan Pierre , Epstein Richard , Poon Ronnie Tung Ping
Published: March 2010

Systemic chemotherapy has had a disappointing track record in the management of advanced hepatocellular carcinoma (HCC). Single‐agent doxorubicin produces a response rate of 10–15%, but without any survival benefit, and combination chemotherapy has also yielded unimpressive results. With recent advances in the knowledge of hepato‐carcinogenesis, there has been encouraging development in the systemic therapy of advanced HCC patients, and particularly in the targeted therapy of advanced HCC. Among the newly identified targets, exciting results have been shown in targeting the anti‐angiogenic pathway and the Raf/mitogen‐activated protein kinase pathways. Bevacizumab, both as a single agent and in combination with other agents, has shown initial encouraging activity in treating advanced HCC. More recently, single‐agent sorafenib, a putative multitargeted kinase inhibitor, has shown to prolong the overall survival of patients with advanced HCC in the pivotal phase III Sorafenib HCC Assessment Randomized Protocol (SHARP) and Oriental study. Currently, sorafenib is the only approved targeted therapy for patients with advanced HCC. In addition, however, promising early results have been reported for other molecular‐targeted drugs including erlotinib and sunitinib. Future progress seems likely to depend on using controlled clinical trials to optimize synergistic combination treatments.
MRI Features of Pontine Autosomal Dominant Microangiopathy and Leukoencephalopathy (PADMAL)
Authors: Ding Xiao‐Qi , Hagel Christian , Ringelstein E. Bernd , Buchheit Stefan , Zeumer Hermann , Kuhlenbäumer Gregor , Appenzeller Silke , Fiehler Jens
Published: March 2010

BACKGROUND AND PURPOSE

Cerebral small vessel disease is a topic of growing interest for both the scientific community and the aging society. We report the magnetic resonance imaging (MRI) characteristics of a recently found autosomal dominantly inherited microangiopathy.

METHODS

Eighteen members (35 to 77 years) of a large German family underwent MR scanning with a standardized MRI protocol for cerebrovascular diseases. Images were evaluated independently by two neuroradiologists.

RESULTS

Six family members revealed an unequivocally pathological phenotype on MRI with lacunar infarcts of the pons (6/6) and lesions of the subcortical and periventricular white matter (5/6). Lesions in the temporal lobes (1/6) and cerebral microbleeds (1/6) were uncommon. None of the patients revealed atherosclerotic changes in MR angiography. Retrospective analysis of 5 brain autopsies from previously reported patients of the same family confirmed the regular involvement of the pons.

CONCLUSION

This cerebral autosomal dominant arteriopathy with pontine infarcts and leukoencephalopathy is characterized by a special lesion pattern strikingly different from CADASIL. The distinct MRI characteristics with pontine lesions and rare occurrence of temporal lesions argue for a new nosological entity and may be helpful for the differential diagnosis.
Seizure‐Induced Inflammation in Focal Cortical Dysplasia Resulting in Imaging Progression That Simulates Neoplasia
Authors: Owens Cormac , Bradley Lisa , Farrell Michael , O’Brien Donncha , King Mary D. , Ryan Stephanie P.
Published: March 2010

A 5‐year‐old girl with previously well‐controlled partial epilepsy secondary to focal cortical dysplasia (FCD) developed an increase in seizure frequency. Two months later, magnetic resonance showed a substantial alteration in lesion imaging characteristics. The lesion was resected. FCD was confirmed but inflammatory changes were also present. We propose that chronic inflammation was induced by unremitting seizure activity and suggest that inflammation may be implicated as a basis for alteration in the imaging characteristics of FCD.
Detection of Right‐to‐Left Shunts may be Associated with Body Size
Authors: Iguchi Yasuyuki , Kimura Kazumi , Kobayashi Kazuto , Aoki Junya , Sakai Kenichiro , Terasawa Yuka , Uemura Junichi , Shibazaki Kensaku
Published: March 2010

BACKGROUND AND PURPOSE

The aim of this study was to investigate whether physiological factors, including body mass index (BMI), are associated with detection of right‐to‐left shunt (RLS) by contrast transcranial Doppler ultrasonography (c‐TCD).

METHODS

After prospective c‐TCD for stroke patients, we compared clinical backgrounds between patients with positive and negative results for RLS. After counting microembolic signals (MES), RLS were functionally graded as follows (grade 0 = 0 MES, grade I = 1‐10 MES, grade II = 11‐30 MES, grade III = 31‐100 MES if countable, grade IV = over 100 MES or uncountable like a shower.

RESULTS

Subjects comprised 584 patients (203 men, 381 women) with a mean age of 67.9 ± 11.1 years. RLS was detected in 134 of 584 patients (23%). In univariate analysis, mean BMI was 22.1 in patients with RLS and 23.3 in those without RLS (P= .004). Mean BMI in concordance with RLS grade gradually decreased (grade 0; 22.7, grade I; 20.8, grade II; 20.1, grade III; 19.6, P= .001). After performing the Valsalva maneuver, mean BMI in concordance with RLS grade linearly increased (grade I; 20.6, grade II; 23.2, grade III; 24.8, grade IV; 25.8, P < .001).

CONCLUSION

Although smaller body size may be associated with detection of RLS, a patient with significant RLS (grade III or IV) had larger body.
Screening for vancomycin‐resistant enterococci: results of a survey in Stockholm
Authors: FANG HONG , NORD CARL ERIK , ULLBERG MÅNS
Published: March 2010

Fang H, Nord CE, Ullberg M. Screening for vancomycin‐resistant enterococci: results of a survey in Stockholm. APMIS 2010; 118: 413–7.

Vancomycin‐resistant enterococci (VRE) are emerging in Stockholm hospitals. To rapidly screen for VRE from stool and rectal swab samples, a detection assay combining broth enrichment and real‐time PCR was set up. From September to December 2008, 6914 samples were screened for VRE using the broth‐PCR combined assay. Of them, 5463 samples were reported as negative the day after sampling. Among the 6914 samples, 47 was screened as vanA probable and 44 of them were confirmed as VRE; 1314 samples was screened as vanB probable and 93 of them were confirmed as VRE. The 44 vanA‐type VRE isolates, detected from 31 patients, were clustered into four genetic types by pulsed‐field gel electrophoresis (PFGE). The same PFGE type was observed in multiple isolates recovered from the same patient with vanA VRE. The 93 vanB‐type VRE isolates were detected from 60 patients, 59 of them harboring VRE with PFGE type 1. One patient with vanB VRE had two isolates of distinct PFGE types (types 1 and 5). PFGE type 1 and PFGE type 2 were predominant clones in vanB and vanA strains, respectively, represented by 98.3% (59/60) of patients with vanB VRE and 77.4% (24/31) of patients with vanA VRE.
Experimental Evaluation of the Transient Behavior of a Compressor Station During Emergency Shutdowns
Authors: Moore J. Jeffrey , Kurz Rainer , Garcia-Hernandez Augusto , Brun Klaus
Published: March 2010

The transient behavior of compressor stations, particularly under rapidly changing conditions, is of vital interest to operators. Predicting transient behavior is an important factor in avoiding damage during events such as emergency shutdowns. A limited number of “accidental” data sets from compressor manufacturers and users are available in the public literature domain. A variety of simulations and modeling approaches have been presented over the last few years at industry conferences. The available experimental data is not of sufficient quality and resolution to properly compare predictions with analytical results or simulations available in current software packages. Necessary information about the compressor, driver, valves, and geometry of the system is often missing. Currently utilized software has not been adequately validated with full-scale realistic benchmark data, as this data is not available in the public domain. Modeling procedures and results of surge control system simulations seldom contain validation data achieved through actual testing. This type of transient test data for a dynamic surge condition is often difficult to obtain. The primary objective of this work is to develop experimental transient compressor surge data on a full-scale test facility, which would facilitate the verification and comparison of existing and future transient surge models. Results of the testing and model comparisons will be documented. Relevant, dimensionless parameters will be presented and validated utilizing the test data. Conclusions from the testing and recommendations for the transient analysis software will be provided.
Combined Cycles With CO2 Capture: Two Alternatives for System Integration
Authors: Sipöcz Nikolett , Assadi Mohsen
Published: March 2010

As carbon capture and storage technology has grown as a promising option to significantly reduce CO2 emissions, system integration and optimization claim an important and crucial role. This paper presents a comparative study of a gas turbine cycle with postcombustion CO2 separation using an amine-based absorption process with monoethanolamine. The study has been made for a triple pressure reheated 400 MWe natural gas-fuelled combined cycle with exhaust gas recirculation (EGR) to improve capture efficiency. Two different options for the energy supply to the solvent regeneration have been evaluated and compared concerning plant performance. In the first alternative heat is provided by steam extracted internally from the bottoming steam cycle, while in the second option an external biomass-fuelled boiler was utilized to generate the required heat. With this novel configuration the amount of CO2 captured can be even more than 100% if the exhaust gas from the biofuelled boiler is mixed and cleaned together with the main exhaust gas flow from the combined cycle. In order to make an unprejudiced comparison between the two alternatives, the reduced steam turbine efficiency has been taken into consideration and estimated, for the alternative with internal steam extraction. The cycles have been modeled in the commercial heat and mass balance program IPSEPRO™ using detailed component models. Utilizing EGR can double the CO2 content of the exhaust gases and reduce the energy need for the separation process by approximately 2% points. Using an external biomass-fuelled boiler as heat source for amine regeneration turns out to be an interesting option due to high CO2 capture effectiveness. However the electrical efficiency of the power plant is reduced compared with the option with internal steam extraction. Another drawback with the external boiler is the higher investment costs but nevertheless, it is flexibility due to the independency from the rest of the power generation system represents a major operational advantage.
On the Adequacy of Chemiluminescence as a Measure for Heat Release in Turbulent Flames With Mixture Gradients
Authors: Lauer Martin , Sattelmayer Thomas
Published: March 2010

The determination of the heat release in technical flames is commonly done via bandpass filtered chemiluminescence measurements in the wavelength range of OH∗ or CH∗ radicals, which are supposed to be a measure for the heat release rate. However, these indirect heat release measurements are problematic because the measured intensities are the superposition of the desired radical emissions and contributions from the broadband emissions of CO2∗. Furthermore, the chemiluminescence intensities are strongly affected by the local air excess ratio of the flame and the turbulence intensity in the reaction zone. To investigate the influence of these effects on the applicability of chemiluminescence as a measure for the heat release rate in turbulent flames with mixture gradients, a reference method is used, which is based on the first law of thermodynamics. It is shown that although the integral heat release can be correlated with the integral chemiluminescence intensities, the heat release distribution is not properly represented by any signal from OH∗ or CH∗. No reliable information about the spatially resolved heat release can be obtained from chemiluminescence measurements in flames with mixture gradients.
Fabrication of spin-polarized electron emitter with single ⟨110⟩-oriented magnetite whisker
Authors: Okada Morihiro , Neo Youichiro , Mimura Hidenori , Nagai Shigekazu , Hata Koichi
Published: March 2010

Magnetite (Fe3O4) is oxidative resistant and has a half metallic property and is expected to have spintronic applications. In this work, ⟨110⟩-oriented single crystal magnetite whiskers, 30–300 nm in diameter, were synthesized on a stainless steel plate by means of the combustion flame thermal oxidation process. An electron source with this single magnetite whisker was fabricated by using a microsampling instrument in a focused ion beam system. The spin polarization of the electron source was found to be 15% at room temperature by using a Mott electron polarimeter.
Nanoscale surface modification of La0.7Sr0.3MnO3 thin films
Authors: Liu Y. , Monsen Å. F. , Boschker J. E. , Wahlström E. , Borg A. , Tybell T.
Published: March 2010

Nanoscale three-dimensional (3D) surface modifications, by scanning tunneling microscopy under ambient conditions, of La0.7Sr0.3MnO3 thin films have been performed. It was demonstrated that there are well-defined combinations of bias voltages, tunneling current, and scan speeds which allow for controlled surface structuring. Lateral structures with sizes down to 1.5 nm are possible to obtain. Moreover, it is possible to reproducibly control the depth of etching with half a unit cell precision, enabling design of 3D surface structures and control of the surface termination of La0.7Sr0.3MnO3 through etching.
New Method for Monitoring Programmed Cell Death and Differentiation in Submerged
Streptomyces
Cultures
Authors: Yagüe Paula , Manteca Angel , Simon Alejandro , Diaz-Garcia Marta Elena , Sanchez Jesus
Published: March 2010

Vital stains were used in combination with fluorimetry for the elaboration of a new method to quantify
Streptomyces
programmed cell death, one of the key events in
Streptomyces
differentiation. The experimental approach described opens the possibility of designing online protocols for automatic monitoring of industrial fermentations.
Use of the Yeast
Pichia pastoris
as an Expression Host for Secretion of Enterocin L50, a Leaderless Two-Peptide (L50A and L50B) Bacteriocin from
Enterococcus faecium
L50
Authors: Basanta Antonio , Gómez-Sala Beatriz , Sánchez Jorge , Diep Dzung B. , Herranz Carmen , Hernández Pablo E. , Cintas Luis M.
Published: March 2010

In this work, we report the expression and secretion of the leaderless two-peptide (EntL50A and EntL50B) bacteriocin enterocin L50 from
Enterococcus faecium
L50 by the methylotrophic yeast
Pichia pastoris
X-33. The bacteriocin structural genes
entL50A
and
entL50B
were fused to the
Saccharomyces cerevisiae
gene region encoding the mating pheromone α-factor 1 secretion signal (
MF
α

1
s

) and cloned, separately and together (
entL50AB
), into the
P. pastoris
expression and secretion vector pPICZαA, which contains the methanol-inducible alcohol oxidase promoter (P
AOX1
) to express the fusion genes. After transfer into the yeast, the recombinant plasmids were integrated into the genome, resulting in three bacteriocinogenic yeast strains able to produce and secrete the individual bacteriocin peptides EntL50A and EntL50B separately and together. The secretion was efficiently directed by MFα1
s
through the Sec system, and the precursor peptides were found to be correctly processed to form mature and active bacteriocin peptides. The present work describes for the first time the heterologous expression and secretion of a two-peptide non-pediocin-like bacteriocin by a yeast.
Cloning of Separate Meilingmycin Biosynthesis Gene Clusters by Use of Acyltransferase-Ketoreductase Didomain PCR Amplification
Authors: He Yunlong , Sun Yuhui , Liu Tiangang , Zhou Xiufen , Bai Linquan , Deng Zixin
Published: March 2010

Five meilingmycins, A to E, with A as the major component, were isolated from
Streptomyces nanchangensis
NS3226. Through nuclear magnetic resonance (NMR) characterization, meilingmycins A to E proved to be identical to reported milbemycins α11, α13, α14, β1, and β9, respectively. Sequencing of a previously cloned 103-kb region identified three modular type I polyketide synthase genes putatively encoding the last 11 elongation steps, three modification proteins, and one transcriptional regulatory protein for meilingmycin biosynthesis. However, the expected loading module and the first two elongation modules were missing. In meilingmycin, the presence of a methyl group at C-24 and a hydroxyl group at C-25 suggests that the elongation module 1 contains a methylmalonyl-coenzyme A (CoA)-specific acyltransferase (ATp) domain and a ketoreductase (KR) domain. Based on the conserved motifs of the ATp and KR domains, a pair of primers was designed for PCR amplification, and a 1.40-kb expected fragment was amplified, whose sequence shows significant homology with the elongation module 1 of the
aveA1
-encoded enzyme AVES1. A polyketide synthase (PKS) gene encoding one loading and two elongation modules, with a downstream C-5-
O
-methyltransferase gene,
meiD
, was subsequently localized 55 kb apart from the previously sequenced region, and its deletion abolishes meilingmycin production. A series of deletions within the 55-kb intercluster region rules out its involvement in meilingmycin biosynthesis. Furthermore, gene deletion of
meiD
eliminates meilingmycins D and E, with methyls at C-5. Our work provides a more specific strategy for the cloning of modular type I PKS gene clusters. The cloning of the meilingmycin gene clusters paves the way for its pathway engineering.
Effects of Environmental Stress on Stability of Tandem Repeats in
Escherichia coli
O157:H7
Authors: Cooley Michael B. , Carychao Diana , Nguyen Kimberly , Whitehand Linda , Mandrell Robert
Published: March 2010

Multilocus variable-number tandem-repeat analysis (MLVA) is used for source tracking
Escherichia coli
O157:H7 in agricultural environments. Tandem repeats were stable after limited replication but changed after exposure to irradiation, elevated temperatures, and starvation conditions. The pO157 plasmid was frequently lost under these stress conditions. Environmental stresses may increase phylogenetic diversity as measured by MLVA.
Spatially Resolved Characterization of Water and Ion Incorporation in
Bacillus
Spores
Authors: Ghosal Sutapa , Leighton Terrance J. , Wheeler Katherine E. , Hutcheon Ian D. , Weber Peter K.
Published: March 2010

We present the first direct visualization and quantification of water and ion uptake into the core of individual dormant
Bacillus thuringiensis
subsp.
israelensis
(
B. thuringiensis
subsp.
israelensis
) endospores. Isotopic and elemental gradients in the
B. thuringiensis
subsp.
israelensis
spores show the permeation and incorporation of deuterium in deuterated water (D
2
O) and solvated ions throughout individual spores, including the spore core. Under hydrated conditions, incorporation into a spore occurs on a time scale of minutes, with subsequent uptake of the permeating species continuing over a period of days. The distribution of available adsorption sites is shown to vary with the permeating species. Adsorption sites for Li
+
, Cs
+
, and Cl
−
are more abundant within the spore outer structures (exosporium, coat, and cortex) relative to the core, while F
−
adsorption sites are more abundant in the core. The results presented here demonstrate that elemental abundance and distribution in dormant spores are influenced by the ambient environment. As such, this study highlights the importance of understanding how microbial elemental and isotopic signatures can be altered postproduction, including during sample preparation for analysis, and therefore, this study is immediately relevant to the use of elemental and isotopic markers in environmental microbiology and microbial forensics.
HypC, the Anthrone Oxidase Involved in Aflatoxin Biosynthesis
Authors: Ehrlich Kenneth C. , Li Ping , Scharfenstein Leslie , Chang Perng-Kuang
Published: March 2010

On the basis of gene disruption and enzyme activity,
hypC
, an open reading frame in the region between the
pksA
(
aflC
) and
nor-1
(
aflD
) genes in the aflatoxin biosynthesis gene cluster, encodes a 17-kDa oxidase that converts norsolorinic acid anthrone to norsolorinic acid.
The Internal Transcribed Spacer Region, a New Tool for Use in Species Differentiation and Delineation of Systematic Relationships within the
Campylobacter
Genus
Authors: Man Si Ming , Kaakoush Nadeem O. , Octavia Sophie , Mitchell Hazel
Published: March 2010

The
Campylobacter
genus consists of a number of important human and animal pathogens. Although the 16S rRNA gene has been used extensively for detection and identification of
Campylobacter
species, there is currently limited information on the 23S rRNA gene and the internal transcribed spacer (ITS) region that lies between the 16S and 23S rRNA genes. We examined the potential of the 23S rRNA gene and the ITS region to be used in species differentiation and delineation of systematic relationships for 30 taxa within the
Campylobacter
genus. The ITS region produced the highest mean pairwise percentage difference (35.94%) compared to the 16S (5.34%) and 23S (7.29%) rRNA genes. The discriminatory power for each region was further validated using Simpson's index of diversity (
D
value). The
D
values were 0.968, 0.995, and 0.766 for the ITS region and the 23S and 16S rRNA genes, respectively. A closer examination of the ITS region revealed that
Campylobacter concisus
,
Campylobacter showae
, and
Campylobacter fetus
subsp.
fetus
harbored tRNA configurations not previously reported for other members of the
Campylobacter
genus. We also observed the presence of strain-dependent intervening sequences in the 23S rRNA genes. Neighbor-joining trees using the ITS region revealed that
Campylobacter jejuni
and
Campylobacter coli
strains clustered in subgroups, which was not observed in trees derived from the 16S or 23S rRNA gene. Of the three regions examined, the ITS region is by far the most cost-effective region for the differentiation and delineation of systematic relationships within the
Campylobacter
genus.
Different Atmospheric Methane-Oxidizing Communities in European Beech and Norway Spruce Soils
Authors: Degelmann Daniela M. , Borken Werner , Drake Harold L. , Kolb Steffen
Published: March 2010

Norway spruce (
Picea abies
) forests exhibit lower annual atmospheric methane consumption rates than do European beech (
Fagus sylvatica
) forests. In the current study,
pmoA
(encoding a subunit of membrane-bound CH
4
monooxygenase) genes from three temperate forest ecosystems with both beech and spruce stands were analyzed to assess the potential effect of tree species on methanotrophic communities. A
pmoA
sequence difference of 7% at the derived protein level correlated with the species-level distance cutoff value of 3% based on the 16S rRNA gene. Applying this distance cutoff, higher numbers of species-level
pmoA
genotypes were detected in beech than in spruce soil samples, all affiliating with upland soil cluster α (USCα). Additionally, two deep-branching genotypes (named 6 and 7) were present in various soil samples not affiliating with
pmoA
or
amoA
. Abundance of USCα
pmoA
genes was higher in beech soils and reached up to (1.2 ± 0.2) × 10
8
pmoA
genes per g of dry weight. Calculated atmospheric methane oxidation rates per cell yielded the same trend. However, these values were below the theoretical threshold necessary for facilitating cell maintenance, suggesting that USCα species might require alternative carbon or energy sources to thrive in forest soils. These collective results indicate that the methanotrophic diversity and abundance in spruce soils are lower than those of beech soils, suggesting that tree species-related factors might influence the
in situ
activity of methanotrophs.
Poor Invasion of Trophoblastic Cells but Normal Plaque Formation in Fibroblastic Cells despite
actA
Deletion in a Group of
Listeria monocytogenes
Strains Persisting in Some Food Processing Environments
Authors: Holch Anne , Gottlieb Caroline Trebbien , Larsen Marianne Halberg , Ingmer Hanne , Gram Lone
Published: March 2010

We determined mammalian cell invasion and virulence gene (
inlA
,
inlB
, and
actA
) sequences of
Listeria monocytogenes
strains belonging to a molecular subtype (RAPD 9) that often persists in Danish fish-processing plants. These strains invaded human placental trophoblasts less efficiently than other
L. monocytogenes
strains, including clinical strains, and they carry a premature stop codon in
inlA
. Eight of 15 strains, including the RAPD 9 and maternofetal strains, had a 105-nucleotide deletion in
actA
that did not affect cell-to-cell spread in mouse fibroblasts. The RAPD 9 strains may still be regarded as of low virulence with respect to human listeriosis.
Development of a Conditional Gene Expression System Using a Zearalenone-Inducible Promoter for the Ascomycete Fungus
Gibberella zeae
Authors: Lee Jungkwan , Son Hokyoung , Lee Seunghoon , Park Ae Ran , Lee Yin-Won
Published: March 2010

The ascomycete fungus
Gibberella zeae
is an important plant pathogen that causes fusarium head blight on small grains. Molecular studies of this fungus have been performed extensively to uncover the biological mechanisms related to pathogenicity, toxin production, and sexual reproduction. Molecular methods, such as targeted gene deletion, gene overexpression, and gene fusion to green fluorescent protein (GFP), are relatively easy to perform with this fungus; however, conditional expression systems have not been developed. The purpose of this study was to identify a promoter that could be induced by zearalenone (ZEA) for the development of a conditional expression system in
G. zeae
. Through microarray analysis, we isolated one zearalenone response gene (
ZEAR
) whose expression was increased more than 50 times after ZEA treatment. Northern blot analysis showed that the
ZEAR
transcript dramatically increased after 1 h of ZEA treatment. To determine the utility of the
ZEAR
promoter, called Pzear, in a conditional expression system, we transformed a
Pzear
::
GFP
fusion construct into
G. zeae
. Our data showed a ZEA concentration-dependent increase in GFP expression. We also replaced the promoter of
G. zeae metE
(
GzmetE)
, an essential gene for methionine biosynthesis, with the Pzear promoter. The growth of the
Pzear-GzmetE
mutant on minimal medium was dependent on the ZEA concentration supplemented in the medium and showed that GzMetE expression was induced by ZEA. This study is the first report of an inducible promoter in
G. zeae.
Our system will be useful for the characterization of essential gene functions in this fungus through differential and ZEA-dependent gene expression. In addition, the Pzear promoter may be applicable as a biosensor for the detection of ZEA contamination in agricultural products.
Comparative Transcriptomic and Phenotypic Analysis of the Responses ofBacillus cereusto Various Disinfectant Treatments
Authors: Ceragioli Mara , Mols Maarten , Moezelaar Roy , Ghelardi Emilia , Senesi Sonia , Abee Tjakko
Published: March 2010

Antimicrobial chemicals are widely applied to clean and disinfect food-contacting surfaces. However, the cellular response of bacteria to various disinfectants is unclear. In this study, the physiological and genome-wide transcriptional responses ofBacillus cereusATCC 14579 exposed to four different disinfectants (benzalkonium chloride, sodium hypochlorite, hydrogen peroxide, and peracetic acid) were analyzed. For each disinfectant, concentrations leading to the attenuation of growth, growth arrest, and cell death were determined. The transcriptome analysis revealed thatB. cereus, upon exposure to the selected concentrations of disinfectants, induced common and specific responses. Notably, the common response included genes involved in the general and oxidative stress responses. Exposure to benzalkonium chloride, a disinfectant known to induce membrane damage, specifically induced genes involved in fatty acid metabolism. Membrane damage induced by benzalkonium chloride was confirmed by fluorescence microscopy, and fatty acid analysis revealed modulation of the fatty acid composition of the cell membrane. Exposure to sodium hypochlorite induced genes involved in metabolism of sulfur and sulfur-containing amino acids, which correlated with the excessive oxidation of sulfhydryl groups observed in sodium hypochlorite-stressed cells. Exposures to hydrogen peroxide and peracetic acid induced highly similar responses, including the upregulation of genes involved in DNA damage repair and SOS response. Notably, hydrogen peroxide- and peracetic acid-treated cells exhibited high mutation rates correlating with the induced SOS response.
Genetic Basis of Tetracycline Resistance in
Bifidobacterium animalis
subsp.
lactis
Authors: Gueimonde Miguel , Flórez Ana Belén , van Hoek Angela H. A. M. , Stuer-Lauridsen Birgitte , Strøman Per , de los Reyes-Gavilán Clara G. , Margolles Abelardo
Published: March 2010

All strains of
Bifidobacterium animalis
subsp.
lactis
described to date show medium level resistance to tetracycline. Screening of 26 strains from a variety of sources revealed the presence of
tet
(W) in all isolates. A transposase gene upstream of
tet
(W) was found in all strains, and both genes were cotranscribed in strain IPLAIC4. Mutants with increased tetracycline resistance as well as tetracycline-sensitive mutants of IPLAIC4 were isolated and genetically characterized. The native
tet
(W) gene was able to restore the resistance phenotype to a mutant with an alteration in
tet
(W) by functional complementation, indicating that
tet
(W) is necessary and sufficient for the tetracycline resistance seen in
B. animalis
subsp.
lactis
.
Constitutive Secretion in Tetrahymena thermophila
Authors: Madinger Catherine L. , Collins Kathleen , Fields Lauren G. , Taron Christopher H. , Benner Jack S.
Published: March 2010

The growth, survival, and life cycle progression of the freshwater ciliated protozoan
Tetrahymena thermophila
are responsive to protein signals thought to be released by constitutive secretion. In addition to providing insights about ciliate communication, studies of constitutive secretion are of interest for evaluating the utility of
T. thermophila
as a platform for the expression of secreted protein therapeutics. For these reasons, we undertook an unbiased investigation of
T. thermophila
secreted proteins using wild-type and secretion mutant strains. Extensive tandem mass spectrometry analyses of secretome samples were performed. We identified a total of 207 secretome proteins, most of which were not detected in a set of abundant whole-cell protein identifications. Numerous proteases and other hydrolases were secreted from cells grown in rich medium but not cells transferred to a nutrient starvation condition. On the other hand, we detected the starvation-enhanced secretion of a small number of cytosolic proteins, suggestive of an exosome-like pathway in
T. thermophila
. Subsets of proteins from the
T. thermophila
regulated secretion pathway were detected with differential representation across strains and culture conditions. Finally, many secretome proteins had a predicted N-terminal signal sequence but no other annotated characteristic or functional classification. Our work provides the first comprehensive analysis of secreted proteins in
T. thermophila
and establishes the groundwork for future studies of constitutive protein secretion biology and biotechnology in ciliates.
Interaction of the Aspergillus nidulans Microtubule-Organizing Center (MTOC) Component ApsB with Gamma-Tubulin and Evidence for a Role of a Subclass of Peroxisomes in the Formation of Septal MTOCs
Authors: Zekert Nadine , Veith Daniel , Fischer Reinhard
Published: March 2010

Peroxisomes are a diverse class of organelles involved in different physiological processes in eukaryotic cells. Although proteins imported into peroxisomes carry a peroxisomal targeting sequence at the C terminus (PTS1) or an alternative one close to the N terminus (PTS2), the protein content of peroxisomes varies drastically. Here we suggest a new class of peroxisomes involved in microtubule (MT) formation. Eukaryotic cells assemble MTs from distinct points in the cell. In the fungus
Aspergillus nidulans
, septum-associated microtubule-organizing centers (sMTOCs) are very active in addition to the spindle pole bodies (SPBs). Previously, we identified a novel MTOC-associated protein, ApsB (
Schizosaccharomyces pombe
mto1), whose absence affected MT formation from sMTOCs more than from SPBs, suggesting that the two protein complexes are organized differently. We show here that sMTOCs share at least two further components, gamma-tubulin and GcpC (
S. pombe
Alp6) with SPBs and found that ApsB interacts with gamma-tubulin. In addition, we discovered that ApsB interacts with the Woronin body protein HexA and is targeted to a subclass of peroxisomes via a PTS2 peroxisomal targeting sequence. The PTS2 motif was necessary for function but could be replaced with a PTS1 motif at the C terminus of ApsB. These results suggest a novel function for a subclass of peroxisomes in cytoskeletal organization.
Analysis of the High-Affinity Iron Uptake System at the Chlamydomonas reinhardtii Plasma Membrane
Authors: Terzulli Alaina , Kosman Daniel J.
Published: March 2010

Multicopper ferroxidases play a vital role in iron metabolism in bacteria, fungi, algae, and mammals.
Saccharomyces cerevisiae
utilizes a channeling mechanism to couple the ferroxidase activity of Fet3p to Fe
3+
transport into the cell by Ftr1p. In contrast, the mechanisms by which mammals couple the ferroxidase reaction to iron trafficking is unclear. The human ferroxidases ceruloplasmin and hephaestin are twice the size of Fet3p and interact with proteins that are not expressed in fungi.
Chlamydomonas
FOX1 is a homolog of the human ferroxidases but likely supports iron uptake in a manner similar to that of yeast, since
Chlamydomonas reinhardtii
expresses a ferric iron permease homolog, FTR1. The results presented support this hypothesis. We show that FOX1 is trafficked to the plasma membrane and is oriented with its multicopper oxidase/ferroxidase domain in the exocytoplasmic space. Our analysis of FTR1 indicates its topology is similar to that of
S. cerevisiae
Ftr1p, with a potential exocytoplasmic iron channeling motif and two potential iron permeation motifs in membrane-spanning regions. We demonstrate that high-affinity iron uptake is dependent on FOX1 and the copper status of the cell. Kinetic inhibition of high-affinity iron uptake by a ferric iron chelator does not reflect the strength of the chelator, supporting a ferric iron channeling mechanism for high-affinity iron uptake in
Chlamydomonas
. Last, recombinant FOX1 (rFOX1) has been isolated in a partially holo form that exhibits the UV-visible absorbance spectrum of a multicopper oxidase and the catalytic activity of a ferroxidase.
Marker Fusion Tagging, a New Method for Production of Chromosomally Encoded Fusion Proteins
Authors: Lai Julian , Ng Seng Kah , Liu Fang Fang , Patkar Rajesh Narhari , Lu Yanfen , Chan Jing Ru , Suresh Angayarkanni , Naqvi Naweed , Jedd Gregory
Published: March 2010

A new gene-tagging method (marker fusion tagging [MFT]) is demonstrated for
Neurospora crassa
and
Magnaporthe oryzae
. Translational fusions between the hygromycin B resistance gene and various markers are inserted into genes of interest by homologous recombination to produce chromosomally encoded fusion proteins. This method can produce tags at any position and create deletion alleles that maintain N- and C-terminal sequences. We show the utility of MFT by producing enhanced green fluorescent protein (EGFP) tags in proteins localized to nuclei, spindle pole bodies, septal pore plugs, Woronin bodies, developing septa, and the endoplasmic reticulum.
Growth Phase-Dependent Activation of the DccRS Regulon of
Campylobacter jejuni
Authors: Wösten Marc M. S. M. , van Dijk Linda , Parker Craig T. , Guilhabert Magalie R. , van der Meer-Janssen Ynske P. M. , Wagenaar Jaap A. , van Putten Jos P. M.
Published: March 2010

Two-component systems are widespread prokaryotic signal transduction devices which allow the regulation of cellular functions in response to changing environmental conditions. The two-component system DccRS (Cj1223c-Cj1222c) of
Campylobacter jejuni
is important for the colonization of chickens. Here, we dissect the DccRS system in more detail and provide evidence that the sensor DccS selectively phosphorylates the cognate effector, DccR. Microarray expression profiling, real-time reverse transcription-PCR (RT-PCR), electrophoretic mobility shift assay, and primer extension analyses revealed that the DccRS regulon of strain 81116 consists of five promoter elements, all containing the consensus direct repeat sequence WTTCAC-N6-TTCACW covering the putative −35 promoter regions. One of these promoters is located in front of an operon encoding a putative macrolide efflux pump while the others are in front of genes coding for putative periplasmic or membrane proteins. The DccRS-regulated genes in
C. jejuni
strain 81116 are needed to enhance early
in vivo
growth of
C. jejuni
in 7-day-old chickens. The DccRS system is activated in the late stationary bacterial growth phase, probably by released metabolic products. Whole-genome mRNA profiling and real-time RT-PCR analysis under these conditions demonstrated that the system has no influence on the transcription of genes outside the DccRS regulon.
Genome Sequence of Hybrid
V
ibrio cholerae
O1 MJ-1236, B-33, and CIRS101 and Comparative Genomics with
V. cholerae
Authors: Grim Christopher J. , Hasan Nur A. , Taviani Elisa , Haley Bradd , Chun Jongsik , Brettin Thomas S. , Bruce David C. , Detter J. Chris , Han Cliff S. , Chertkov Olga , Challacombe Jean , Huq Anwar , Nair G. Balakrish , Colwell Rita R.
Published: March 2010

The genomes of
V
ibrio cholerae
O1 Matlab variant MJ-1236, Mozambique O1 El Tor variant B33, and altered O1 El Tor CIRS101 were sequenced. All three strains were found to belong to the phylocore group 1 clade of
V. cholerae
, which includes the 7th-pandemic O1 El Tor and serogroup O139 isolates, despite displaying certain characteristics of the classical biotype. All three strains were found to harbor a hybrid variant of CTXΦ and an integrative conjugative element (ICE), leading to their establishment as successful clinical clones and the displacement of prototypical O1 El Tor. The absence of strain- and group-specific genomic islands, some of which appear to be prophages and phage-like elements, seems to be the most likely factor in the recent establishment of dominance of
V. cholerae
CIRS101 over the other two hybrid strains.
Complete Genome Sequence of the Probiotic
Lactobacillus casei
Strain BL23
Authors: Mazé Alain , Boël Grégory , Zúñiga Manuel , Bourand Alexa , Loux Valentin , Yebra Maria Jesus , Monedero Vicente , Correia Karine , Jacques Noémie , Beaufils Sophie , Poncet Sandrine , Joyet Philippe , Milohanic Eliane , Casarégola Serge , Auffray Yanick , Pérez-Martínez Gaspar , Gibrat Jean-François , Zagorec Monique , Francke Christof , Hartke Axel , Deutscher Josef
Published: March 2010

The entire genome of
Lactobacillus casei
BL23, a strain with probiotic properties, has been sequenced. The genomes of BL23 and the industrially used probiotic strain Shirota YIT 9029 (Yakult) seem to be very similar.
Complete Genome Sequence of the Thermophilic, Obligately Chemolithoautotrophic Hydrogen-Oxidizing Bacterium
Hydrogenobacter thermophilus
TK-6
Authors: Arai Hiroyuki , Kanbe Haruna , Ishii Masaharu , Igarashi Yasuo
Published: March 2010

Hydrogenobacter thermophilus
is a thermophilic, obligately chemolithoautotrophic and aerobic hydrogen-oxidizing bacterium. It is unique in its ability to fix carbon dioxide via the reductive tricarboxylic acid cycle under aerobic conditions. It utilizes molecular hydrogen, elemental sulfur, or thiosulfate as the sole energy source. Here, we report the complete genome sequence of
H. thermophilus
TK-6.
Complete Genome Sequence and Annotation of the
Treponema pallidum
subsp.
pallidum
Chicago Strain
Authors: Giacani Lorenzo , Jeffrey Brendan M. , Molini Barbara J. , Le HoaVan T. , Lukehart Sheila A. , Centurion-Lara Arturo , Rockey Daniel D.
Published: March 2010

In syphilis research, the Nichols strain of
Treponema pallidum
, isolated in 1912, has been the most widely studied. Recently, important differences among
T. pallidum
strains emerged; therefore, we sequenced and annotated the Chicago strain genome to facilitate and encourage the use of this strain in studying the pathogenesis of syphilis.