bluuebunny/crossref_metadata_2025 huggingface dataset:
The role of RelA (p65) threonine 505 phosphorylation in the regulation of cell growth, survival, and migration
Authors: Msaki Aichi , Sánchez Ana M. , Koh Li Fang , Barré Benjamin , Rocha Sonia , Perkins Neil D. , Johnson Renée F.
Published: July 2011

The NF-κB family of transcription factors is a well-established regulator of the immune and inflammatory responses and also plays a key role in other cellular processes, including cell death, proliferation, and migration. Conserved residues in the trans-activation domain of RelA, which can be posttranslationally modified, regulate divergent NF-κB functions in response to different cellular stimuli. Using rela−/−mouse embryonic fibroblasts reconstituted with RelA, we find that mutation of the threonine 505 (T505) phospho site to alanine has wide-ranging effects on NF-κB function. These include previously described effects on chemotherapeutic drug-induced apoptosis, as well as new roles for this modification in autophagy, cell proliferation, and migration. This last effect was associated with alterations in the actin cytoskeleton and expression of cellular migration–associated genes such as WAVE3 and α-actinin 4. We also define a new component of cisplatin-induced, RelA T505–dependent apoptosis, involving induction of NOXA gene expression, an effect explained at least in part through induction of the p53 homologue, p73. Therefore, in contrast to other RelA phosphorylation events, which positively regulate NF-κB function, we identified RelA T505 phosphorylation as a negative regulator of its ability to induce diverse cellular processes such as apoptosis, autophagy, proliferation, and migration.
The Cardiac Atlas Project—an imaging database for computational modeling and statistical atlases of the heart
Authors: Fonseca Carissa G. , Backhaus Michael , Bluemke David A. , Britten Randall D. , Chung Jae Do , Cowan Brett R. , Dinov Ivo D. , Finn J. Paul , Hunter Peter J. , Kadish Alan H. , Lee Daniel C. , Lima Joao A. C. , Medrano−Gracia Pau , Shivkumar Kalyanam , Suinesiaputra Avan , Tao Wenchao , Young Alistair A.
Published: July 2011

Motivation: Integrative mathematical and statistical models of cardiac anatomy and physiology can play a vital role in understanding cardiac disease phenotype and planning therapeutic strategies. However, the accuracy and predictive power of such models is dependent upon the breadth and depth of noninvasive imaging datasets. The Cardiac Atlas Project (CAP) has established a large-scale database of cardiac imaging examinations and associated clinical data in order to develop a shareable, web-accessible, structural and functional atlas of the normal and pathological heart for clinical, research and educational purposes. A goal of CAP is to facilitate collaborative statistical analysis of regional heart shape and wall motion and characterize cardiac function among and within population groups.

Results: Three main open-source software components were developed: (i) a database with web-interface; (ii) a modeling client for 3D + time visualization and parametric description of shape and motion; and (iii) open data formats for semantic characterization of models and annotations. The database was implemented using a three-tier architecture utilizing MySQL, JBoss and Dcm4chee, in compliance with the DICOM standard to provide compatibility with existing clinical networks and devices. Parts of Dcm4chee were extended to access image specific attributes as search parameters. To date, approximately 3000 de-identified cardiac imaging examinations are available in the database. All software components developed by the CAP are open source and are freely available under the Mozilla Public License Version 1.1 (http://www.mozilla.org/MPL/MPL-1.1.txt).

Availability:  http://www.cardiacatlas.org

Contact:  a.young@auckland.ac.nz

Supplementary information:  Supplementary data are available at Bioinformatics online.
APCluster: an R package for affinity propagation clustering
Authors: Bodenhofer Ulrich , Kothmeier Andreas , Hochreiter Sepp
Published: July 2011

Summary: Affinity propagation (AP) clustering has recently gained increasing popularity in bioinformatics. AP clustering has the advantage that it allows for determining typical cluster members, the so-called exemplars. We provide an R implementation of this promising new clustering technique to account for the ubiquity of R in bioinformatics. This article introduces the package and presents an application from structural biology.

Availability: The R package apcluster is available via CRAN—The Comprehensive R Archive Network: http://cran.r-project.org/web/packages/apcluster

Contact:  apcluster@bioinf.jku.at; bodenhofer@bioinf.jku.at
Simulating systems genetics data with SysGenSIM
Authors: Pinna Andrea , Soranzo Nicola , Hoeschele Ina , de la Fuente Alberto
Published: July 2011

Summary: SysGenSIM is a software package to simulate Systems Genetics (SG) experiments in model organisms, for the purpose of evaluating and comparing statistical and computational methods and their implementations for analyses of SG data [e.g. methods for expression quantitative trait loci (eQTL) mapping and network inference]. SysGenSIM allows the user to select a variety of network topologies, genetic and kinetic parameters to simulate SG data ( genotyping, gene expression and phenotyping) with large gene networks with thousands of nodes. The software is encoded in MATLAB, and a user-friendly graphical user interface is provided.

Availability: The open-source software code and user manual can be downloaded at: http://sysgensim.sourceforge.net/

Contact:  alf@crs4.it
Characterization of the role of the RadS/RadR two-component system in the radiation resistance of Deinococcus radiodurans
Authors: Desai Shruti S. , Rajpurohit Yogendra S. , Misra Hari S. , Deobagkar Dileep N.
Published: July 2011

Deinococcus radiodurans shows extraordinary tolerance to DNA damage, and exhibits differential gene expression and protein recycling. A putative response regulator, the DRB0091 (RadR) ORF, was identified from a pool of DNA-binding proteins induced in response to gamma radiation in this bacterium. radR is located upstream of drB0090, which encodes a putative sensor histidine kinase (RadS) on the megaplasmid. Deletion of these genes both individually and together resulted in hypersensitivity to DNA-damaging agents and a delayed or altered double-strand break repair. A ΔradRradS double mutant and a ΔradR single mutant showed nearly identical responses to gamma radiation and UVC. Wild-type RadR and RadS complemented the corresponding mutant strains, but also exhibited significant cross-complementation, albeit at lower doses of gamma radiation. The radS transcript was not detected in the ΔradR mutant, suggesting the existence of a radRS operon. Recombinant RadS was autophosphorylated and could catalyse the transfer of γ phosphate from ATP to RadR in vitro. These results indicated the functional interaction of RadS and RadR, and suggested a role for the RadS/RadR two-component system in the radiation resistance of this bacterium.
Gentisate 1,2-dioxygenase, in the third naphthalene catabolic gene cluster of Polaromonas naphthalenivorans CJ2, has a role in naphthalene degradation
Authors: Lee Hyo Jung , Kim Jeong Myeong , Lee Se Hee , Park Minjeong , Lee Kangseok , Madsen Eugene L. , Jeon Che Ok
Published: July 2011

Polaromonas naphthalenivorans strain CJ2 metabolizes naphthalene via the gentisate pathway and has recently been shown to carry a third copy of gentisate 1,2-dioxygenase (GDO), encoded by nagI3, within a previously uncharacterized naphthalene catabolic gene cluster. The role of this cluster (especially nagI3) in naphthalene metabolism of strain CJ2 was investigated by documenting patterns in regulation, transcription and enzyme activity. Transcriptional analysis of wild-type cells showed the third cluster to be polycistronic and that nagI3 was expressed at a relatively high level. Individual knockout mutants of all three nagI genes were constructed and their influence on both GDO activity and cell growth was evaluated. Of the three knockout strains, CJ2ΔnagI3 showed severely diminished GDO activity and grew slowest on aromatic substrates. These observations are consistent with the hypothesis that nagI3 may prevent toxic intracellular levels of gentisate from accumulating in CJ2 cells. All three nagI genes from strain CJ2 were cloned into Escherichia coli: the nagI2 and nagI3 genes were successfully overexpressed. The subunit mass of the GDOs were ~36–39 kDa, and their structures were deduced to be dimeric. The K
m values of NagI2 and NagI3 were 31 and 10 µM, respectively, indicating that the higher affinity of NagI3 for gentisate may protect the wild-type cells from gentisate toxicity. These results provide clues for explaining why the third gene cluster, particularly the nagI3 gene, is important in strain CJ2. The organization of genes in the third gene cluster matched that of clusters in Polaromonas sp. JS666 and Leptothrix cholodnii SP-6. While horizontal gene transfer (HGT) is one hypothesis for explaining this genetic motif, gene duplication within the ancestral lineage is equally valid. The HGT hypothesis was discounted by noting that the nagI3 allele of strain CJ2 did not share high sequence identity with its homologues in Polaromonas sp. JS666 and L. cholodnii SP-6.
Aeromonas hydrophila motY is essential for polar flagellum function, and requires coordinate expression of motX and Pom proteins
Authors: Molero Raquel , Wilhelms Markus , Infanzón Belén , Tomás Juan M. , Merino Susana
Published: July 2011

By the analysis of the Aeromonas hydrophila ATCC7966T genome we identified A. hydrophila AH-3 MotY. A. hydrophila MotY, like MotX, is essential for the polar flagellum function energized by an electrochemical potential of Na+ as coupling ion, but is not involved in lateral flagella function energized by the proton motive force. Thus, the A. hydrophila polar flagellum stator is a complex integrated by two essential proteins, MotX and MotY, which interact with one of two redundant pairs of proteins, PomAB and PomA2B2. In an A. hydrophila motX mutant, polar flagellum motility is restored by motX complementation, but the ability of the A. hydrophila motY mutant to swim is not restored by introduction of the wild-type motY alone. However, its polar flagellum motility is restored when motX and -Y are expressed together from the same plasmid promoter. Finally, even though both the redundant A. hydrophila polar flagellum stators, PomAB and PomA2B2, are energized by the Na+ ion, they cannot be exchanged. Furthermore, Vibrio parahaemolyticus PomAB and Pseudomonas aeruginosa MotAB or MotCD are unable to restore swimming motility in A. hydrophila polar flagellum stator mutants.
Interaction between poly(3-hydroxybutyrate) granule-associated proteins as revealed by two-hybrid analysis and identification of a new phasin in Ralstonia eutropha H16
Authors: Pfeiffer Daniel , Jendrossek Dieter
Published: July 2011

A large number of polypeptides are attached to poly(3-hydroxybutyrate) (PHB) granules of Ralstonia eutropha, such as PHB synthase (PhaC1), several PHB depolymerases (PhaZs) and phasins (PhaPs), the regulator protein PhaR
Reu
, and possibly others. In this study we used the bacterial adenylate cyclase-based two-hybrid assay to investigate interactions between known PHB granule-associated proteins (PGAPs) and to screen for new PGAPs. The utility of the system was tested by the in vivo verification of previously postulated interactions of the PHB synthase subunits of R. eutropha (PhaC1 homo-oligomerization) and of Bacillus megaterium (PhaC
Bmeg
–PhaR
Bmeg
hetero-oligomerization). Nine proteins (PhaA, PhaB1, PhaC1, PhaP1–PhaP4, PhaZ1 and PhaR), with established functions in PHB metabolism of R. eutropha, were tested for interaction in all combinations. While no significant interaction was detected between the PHB synthase PhaC1 and any of the other eight tested Pha proteins, strong interactions were found between all phasin proteins, in particular between PhaP2 and PhaP4. When PhaP2 was used as bait in a two-hybrid screening experiment with a genomic library of R. eutropha, the B1934 gene product was identified in 24 out of 53 isolated clones. B1934 encodes a hypothetical protein (15.7 kDa) with similarity to phasins of PHB-accumulating bacteria. A fusion protein of eYfp and the B1934 gene product colocalized with PHB granules, confirming that B1934 represents a new phasin (PhaP5). PhaP5 was not essential for PHB granule formation, but overexpression of PhaP5 increased the number of cells with PHB granules at the cell poles.
Side population cells isolated from human osteosarcoma are enriched with tumor‐initiating cells
Authors: Yang Min , Yan Ming , Zhang Rui , Li Jing , Luo Zhuojing
Published: July 2011

It has been proven that “side population (SP)” cells that exclude Hoechst 33342 dye are enriched with cancer stem cells in several tumors. In the present study we aimed to isolate and characterize SP cells from human primary osteosarcoma. Side population cells were detected in osteosarcoma samples. In vitro, SP cells regenerated both SP and non‐SP and the clonogenicity of SP cells was higher than that of non‐SP cells, just like stem cells. In vivo, SP cells exhibited heightened tumorigenicity and only the SP fraction had the capacity to self‐ renew both in vitro and in vivo. Furthermore, SP cells exhibited increased multidrug resistance and the RNA expression of ATP‐binding cassette protein transporters was increased in the SP group. In addition, “stemness” genes Oct‐4 and Nanog were also upregulated in the SP group. However, the expression of other putative stem cell markers (CD44, CD117 and CD133) had no significant difference between SP and non‐SP for each individual marker. These findings suggest that SP cells derived from osteosarcoma are enriched with tumorigenic cells with stem‐like properties and might be an ideal target for clinical therapy. (Cancer Sci 2011; 102: 1774–1781)
High‐resolution and super stacking of time‐reversal mirrors in locating seismic sources
Authors: Cao W. , Hanafy S. M. , Schuster G. T. , Zhan G. , Boonyasiriwat C.
Published: July 2011

Time reversal mirrors can be used to backpropagate and refocus incident wavefields to their actual source location, with the subsequent benefits of imaging with high‐resolution and super‐stacking properties. These benefits of time reversal mirrors have been previously verified with computer simulations and laboratory experiments but not with exploration‐scale seismic data. We now demonstrate the high‐resolution and the super‐stacking properties in locating seismic sources with field seismic data that include multiple scattering. Tests on both synthetic data and field data show that a time reversal mirror has the potential to exceed the Rayleigh resolution limit by factors of 4 or more. Results also show that a time reversal mirror has a significant resilience to strong Gaussian noise and that accurate imaging of source locations from passive seismic data can be accomplished with traces having signal‐to‐noise ratios as low as 0.001. Synthetic tests also demonstrate that time reversal mirrors can sometimes enhance the signal by a factor proportional to the square root of the product of the number of traces, denoted as N and the number of events in the traces. This enhancement property is denoted as super‐stacking and greatly exceeds the classical signal‐to‐noise enhancement factor of . High‐resolution and super‐stacking are properties also enjoyed by seismic interferometry and reverse‐time migration with the exact velocity model.
Gravity field and tectonic features of Block L2 in the Lamu basin, Kenya
Authors: Yuan Bingqiang , Xie Wensheng , Liu Guihe , Zhang Chunguan
Published: July 2011

A gravity survey on the scale of 1: 250 000 was carried out in Block L2 located in the Lamu basin of south‐east Kenya in order to study tectonic features and find out favourable petroleum prospects in the block. This paper, through data processing and synthetic interpretation of the measured gravity data in the block, discusses characteristics of the gravity field and their geological implications, determines the fault system and the basement depth, analyses features of the main strata, divides structure units and predicts favourable petroleum zones. In the block, the regional gravity anomaly is mainly caused by the inclined Moho surface that rises in the east and subsides in the west topographically and the Bouguer gravity anomaly primarily reflects the superimposition of the gravity effect derived from the Moho surface and the basement relief. Two groups of faults extending NW (NWW) and NE (NEE) respectively are dominant in the block and their activities resulted in the framework of east‐west zoning and south‐north blocking. The basement depth greatly changes in an alternative high and low pattern. The Permian‐Triassic, Jurassic and Tertiary strata are extensively developed, while the Cretaceous is only developed in the east of the block. Structurally, the block can be divided into five units, of which the Tana sag shows excellent source‐reservoir‐seal associations and is a favourable target for future petroleum exploration.
Geophones on blocks: a prototype towable geophone system for shallow land seismic investigations
Authors: Moura Rui M. , Senos Matias Manuel J.
Published: July 2011

In recent years some authors have given a certain amount of attention to towed seismic reflection acquisition systems. Based on some of these works we sought to design and test a system making use of currently available geophones instead of specifically designed sensors as employed in some previous works. Thus, bearing in mind that the geophone's characteristics are achieved in the conditions that they are originally designed to be employed in, i.e., coupled with a spike driven into the ground, we devoted our attention to some of the variables involved in the geophone's performance, namely the total weight, the effect of a spikeless geophone and the surfaces on which the geophone is placed. Previously, we had experimentally verified some variations in the signal response due to coupling geophones in different surface materials, such as hard soil, asphalt and concrete pavement and we noticed that these surface materials were in fact an important factor in the overall response. Hence, these materials, or as we also called them coupling agents, could be employed as a base material in the construction of a mobile seismic acquisition device composed of blocks of a certain size, on which the geophone would be then inserted and thus making it into a spikeless surface towable system. Therefore, various materials were tested in order to select one that could maintain a similar fidelity to that of the spike coupled geophone and thus contribute towards building a more time efficient and towable geophone and block system. Pinging tests revealed variations in the coupling frequency and damping characteristics of each coupling agent and from all of these tested materials one was selected for field comparative tests with the normally planted geophones with spike coupling. Finally a seismic reflection profile was acquired simultaneously with both systems, i.e., spike coupling versus cement block coupled geophones.

This field test showed similar results in terms of signal levels and frequency content and therefore it was possible to observe the presence of the same reflectors and other seismic events in either of the time sections.

With this experiment we propose not only a system that allows a time efficient seismic field operation but we also aim to encourage more research into the response dependency of the coupling agent of which the towable base block is made of.
Application of 3D vertical seismic profile multi‐component data to tight gas sands‡
Authors: Yan Yousheng , Xu Zengkui , Yi Mingli , Wei Xin
Published: July 2011

Due to the complicated geophysical character of tight gas sands in the Sulige gasfield of China, conventional surface seismic has faced great challenges in reservoir delineation. In order to improve this situation, a large‐scale 3D‐3C vertical seismic profiling (VSP) survey (more than 15 000 shots) was conducted simultaneously with 3D‐3C surface seismic data acquisition in this area in 2005. This paper presents a case study on the delineation of tight gas sands by use of multi‐component 3D VSP technology. Two imaging volumes (PP compressional wave; PSv converted wave) were generated with 3D‐3C VSP data processing. By comparison, the dominant frequencies of the 3D VSP images were 10–15 Hz higher than that of surface seismic images. Delineation of the tight gas sands is achieved by using the multi‐component information in the VSP data leading to reduce uncertainties in data interpretation. We performed a routine data interpretation on these images and developed a new attribute titled ‘Centroid Frequency Ratio of PSv and PP Waves’ for indication of the tight gas sands. The results demonstrated that the new attribute was sensitive to this type of reservoir. By combining geologic, drilling and log data, a comprehensive evaluation based on the 3D VSP data was conducted and a new well location for drilling was proposed. The major results in this paper tell us that successful application of 3D‐3C VSP technologies are only accomplished through a synthesis of many disciplines. We need detailed analysis to evaluate each step in planning, acquisition, processing and interpretation to achieve our objectives. High resolution, successful processing of multi‐component information, combination of PP and PSv volumes to extract useful attributes, receiver depth information and offset/ azimuth‐dependent anisotropy in the 3D VSP data are the major accomplishments derived from our attention to detail in the above steps.
Florfenicol pharmacokinetics in healthy adult alpacas after subcutaneous and intramuscular injection
Authors: HOLMES K. , BEDENICE D. , PAPICH M. G.
Published: July 2011

Holmes, K., Bedenice, D., Papich, M. G. Florfenicol pharmacokinetics in healthy adult alpacas after subcutaneous and intramuscular injection.J. vet. Pharmacol. Therap. 35, 382–388.

A single dose of florfenicol (Nuflor®) was administered to eight healthy adult alpacas at 20 mg/kg intramuscular (i.m.) and 40 mg/kg subcutaneous (s.c.) using a randomized, cross‐over design, and 28‐day washout period. Subsequently, 40 mg/kg florfenicol was injected s.c. every other day for 10 doses to evaluate long‐term effects. Maximum plasma florfenicol concentrations (Cmax, measured via high‐performance liquid chromatography) were achieved rapidly, leading to a higher Cmaxof 4.31 ± 3.03 μg/mL following administration of 20 mg/kg i.m. than 40 mg/kg s.c. (Cmax: 1.95 ± 0.94 μg/mL). Multiple s.c. dosing at 48 h intervals achieved a Cmaxof 4.48 ± 1.28 μg/mL at steady state. The area under the curve and terminal elimination half‐lives were 51.83 ± 11.72 μg/mL·h and 17.59 ± 11.69 h after single 20 mg/kg i.m. dose, as well as 99.78 ± 23.58 μg/mL·h and 99.67 ± 59.89 h following 40 mg/kg injection of florfenicol s.c., respectively. Florfenicol decreased the following hematological parameters after repeated administration between weeks 0 and 3: total protein (6.38 vs. 5.61 g/dL,P < 0.0001), globulin (2.76 vs. 2.16 g/dL,P < 0.0003), albumin (3.61 vs. 3.48 g/dL,P = 0.0038), white blood cell count (11.89 vs. 9.66 × 103/μL,P < 0.044), and hematocrit (27.25 vs. 24.88%,P < 0.0349). Significant clinical illness was observed in one alpaca. The lowest effective dose of florfenicol should thus be used in alpacas and limited to treatment of highly susceptible pathogens.
Streptococcus pyogenes antigen I/II‐family polypeptide AspA shows differential ligand‐binding properties and mediates biofilm formation
Authors: Maddocks Sarah E. , Wright Christopher J. , Nobbs Angela H. , Brittan Jane L. , Franklin Linda , Strömberg Nicklas , Kadioglu Aras , Jepson Mark A. , Jenkinson Howard F.
Published: July 2011

The streptococcal antigen I/II (AgI/II)‐family polypeptides are cell wall‐anchored adhesins expressed by most indigenous oral streptococci. Proteins sharing 30–40% overall amino acid sequence similarities with AgI/II‐family proteins are also expressed by Streptococcus pyogenes. The S. pyogenes M28_Spy1325 polypeptide (designated AspA) displays an AgI/II primary structure, with alanine‐rich (A) and proline‐rich (P) repeats flanking a V region that is projected distal from the cell. In this study it is shown that AspA from serotype M28 S. pyogenes, when expressed on surrogate host Lactococcus lactis, confers binding to immobilized salivary agglutinin gp‐340. This binding was blocked by antibodies to the AspA‐VP region. In contrast, the N‐terminal region of AspA was deficient in binding fluid‐phase gp‐340, and L. lactis cells expressing AspA were not agglutinated by gp‐340. Deletion of the aspA gene from two different M28 strains of S. pyogenes abrogated their abilities to form biofilms on saliva‐coated surfaces. In each mutant strain, biofilm formation was restored by trans complementation of the aspA deletion. In addition, expression of AspA protein on the surface of L. lactis conferred biofilm‐forming ability. Taken collectively, the results provide evidence that AspA is a biofilm‐associated adhesin that may function in host colonization by S. pyogenes.
The cop operon is required for copper homeostasis and contributes to virulence in Streptococcus pneumoniae
Authors: Shafeeq Sulman , Yesilkaya Hasan , Kloosterman Tomas G. , Narayanan Geetha , Wandel Michal , Andrew Peter W. , Kuipers Oscar P. , Morrissey Julie A.
Published: July 2011

High levels of copper are toxic and therefore bacteria must limit free intracellular levels to prevent cellular damage. In this study, we show that a number of pneumococcal genes are differentially regulated by copper, including an operon encoding a CopY regulator, a protein of unknown function (CupA) and a P1‐type ATPase, CopA, which is conserved in all sequenced Streptococcus pneumoniae strains. Transcriptional analysis demonstrated that the cop operon is induced by copper in vitro, repressed by the addition of zinc and is autoregulated by the copper‐responsive CopY repressor protein. We also demonstrate that the CopA ATPase is a major pneumococcal copper resistance mechanism and provide the first evidence that the CupA protein plays a role in copper resistance. Our results also show that copper homeostasis is important for pneumococcal virulence as the expression of the cop operon is induced in the lungs and nasopharynx of intranasally infected mice, and a copA‐ mutant strain, which had decreased growth in high levels of copper in vitro, showed reduced virulence in a mouse model of pneumococcal pneumonia. Furthermore, using the copA‐ mutant we observed for the first time in any bacteria that copper homeostasis also appears to be required for survival in the nasopharynx.
Photoperiodic response in the subtropical and warm‐temperate zone populations of the southern green stink bug Nezara viridula: why does it not fit the common latitudinal trend?
Authors: MUSOLIN DMITRY L. , TOUGOU DAISUKE , FUJISAKI KENJI
Published: July 2011

The photoperiodic response of diapause induction is studied in females of five subtropical and warm‐temperate zone populations of Nezara viridula (L.) (Heteroptera: Pentatomidae) in Japan (26.4–34.7°N; 127.4–135.7°E). Laboratory tests at 25 °C demonstrate that both warm‐temperate and subtropical populations have pronounced photoperiodic responses of adult diapause induction. Under short‐day conditions (LD 10 : 14 h), 73–100% of females enter diapause, whereas, under long‐day conditions (LD 15 : 9 h), 87–100% of females are nondiapause and reproduce. When the critical photoperiod for diapause induction is plotted against the latitude of origin of each population, the data points do not show the expected tendency of increasing critical photoperiod northwards but, instead, vary between 12 h 15 min and 13 h 30 min. It is suggested that adults from different populations of such a highly migratory species move often among subtropical islands (by themselves or being assisted by typhoons), thus constantly destabilizing the photoperiodic responses. Although important for general synchronization of seasonal development in the tropics and subtropics, winter diapause might not be so critical for survival in mild winters in these zones. Such circumstances might make the selective pressure over the photoperiodic response less severe in the tropics and subtropics than in the temperate zone. It is suggested that the current climate warming might contribute to this situation as well by promoting polewards migrations and lessening the selective pressure of overwintering conditions.
Comment on ‘Insights from the Mw 6.3, 2009 L’Aquila earthquake (central Apennines) to unveil new seismogenic sources through their surface signature: the adjacent San Pio Fault’ by Bucciet al.(2011)
Authors: Messina Paolo , Galli Paolo , Giaccio Biagio
Published: July 2011

Terra Nova, 23, 280–282, 2011

We question the approach followed by the Authors in identifying a presumed ‘new’ fault, and particularly the uncritical use made of topographic profiles, in which morphological features of different ages and origins are crudely correlated, creating the fake image of fault‐tilting. We also point out the incorrect age attribution of faulted deposits – assumed without any analytical determination and/or stratigraphical framework – which has yielded serious errors as far as the timing of fault activity is concerned. These mistakes have led to incorrect conclusions and unavoidable repercussions for seismic hazard assessment of a region which has been just tragically struck by a disruptive earthquake.
Simultaneous detection of HFE C282Y, H63D and S65C mutations associated with type 1 haemochromatosis using a multiplex luminex bead assay
Authors: Cardoso S. P. , Patel R. , Brown C. , Navarrete C.
Published: July 2011

Type 1 hereditary haemochromatosis (HH) is a common genetic disorder in Caucasoids resulting from mutations in the HFE gene. Routine diagnostic testing for type 1 HH involves genotyping for two of these described HFE mutations, C282Y and H63D. In some cases typing of a third mutation, S65C is also performed. Several techniques have been reported for HFE genotyping and these include polymerase chain reaction (PCR)‐sequence‐specific primers (SSP), PCR‐restriction fragment length polymorphism (RFLP), PCR‐sequence‐specific oligonucleotide probe (SSOP), real‐time PCR followed by melting curve analysis and TaqMan assay. The aim of this study was to develop an alternative method to both conventional PCR and real‐time PCR/TaqMan assay to detect all three HFE mutations in a single assay using Luminex technology. DNA controls of known genotypes (n = 109) were used to evaluate this approach. These controls were selected to represent the three possible genotypes (wild type, mutant, heterozygous) for each mutation. Subsequently, blind DNA samples (n = 100) were used to validate this method. This new assay was then compared with current techniques (in‐house PCR‐SSP and TaqMan assay). Comparison of genotypes obtained with the Luminex method with those previously reported by both in‐house PCR‐SSP and TaqMan assay showed 100% concordance for both DNA controls and blind DNA samples and no discrepancies were observed. Allelic frequency for C282Y, H63D and S65C mutations were 22%, 16% and 2%, respectively. We report here a high‐throughput, accurate and robust multiplex luminex bead assay for routine clinical testing of C282Y, H63D and S65C mutations in the HFE gene.
Inflammatory polyps following successful HLA‐matched cord blood transplantation in a patient with X‐linked lymphoproliferative syndrome
Authors: Buchbinder David , Younes Bassam , Sassoon Aaron , Soni Amit , Hsieh Loan , Puthenveetil Geetha , Stites Jill , Ness‐Jorden Tristen , Neudorf Steven , Nugent Diane
Published: July 2011

Buchbinder D, Younes B, Sassoon A, Soni A, Hsieh L, Puthenveetil G, Stites J, Ness‐Jorden T, Neudorf S, Nugent D. Inflammatory polyps following successful HLA‐matched cord blood transplantation in a patient with X‐linked lymphoproliferative syndrome.

Abstract:  Gastrointestinal complications following HSCT are numerous and include a variety of issues resulting in hepatic, biliary, pancreatic, and intestinal compromise. In the context of an underlying state of immune dysregulation, novel complications may arise including autoimmunity. To our knowledge, this is the first report of a patient with XLP who was successfully treated with HSCT using an HLA‐matched unrelated cord blood unit that was complicated by the development of inflammatory polyps of the colon. Given the underlying diagnosis of XLP and its associated immune dysregulation, the challenge of understanding unique gastrointestinal manifestations of autoimmunity following HSCT is discussed.
Pyrosequencing of a hypervariable region in the internal transcribed spacer 2 to identify clinical yeast isolates
Authors: Pannanusorn Srisuda , Elings Marlene Axner , Römling Ute , Fernandez Victor
Published: July 2011

The incidence of invasive fungal infection has increased significantly. A majority of the infections is caused by yeast. Clinically important yeast show species‐specific differences in susceptibility to antifungal agents therefore rapid and accurate identification of the pathogen is essential. We aimed to validate pyrosequencing of 40 nucleotides in the internal transcribed spacer 2 (ITS2) for species identification of yeast. Amplification of ITS2 and pyrosequencing of targeted region were performed in 940 clinical isolates of yeast. A local database containing the 40 nucleotide ITS2 sequences of 33 species of medically important yeast was generated using published sequences of type strains. The sequencing results were searched against the local database using the BLAST algorithm to identify the species of yeast. The length of sequences obtained from pyrosequencing averaged between 40–61 nucleotides. Pyrosequencing identified 940 clinical isolates of yeast down to 14 species level, whereby 931 isolates belonged to genus Candida (11 species), four of Saccharomyces cerevisiae, three of Malassezia pachydermatis and two of Rhodotorula mucilaginosa. In addition, intraspecies specific sequence variations in Candida albicans and Candida glabrata were detected. Pyrosequencing of 40 nucleotides in ITS2 is reliable for species identification of yeast. This methodology can contribute to the high quality management of patients with fungal infections.
Effect of peritoneal dialysis on expression of vascular endothelial growth factor, basic fibroblast growth factor and endostatin of the peritoneum in peritoneal dialysis patients
Authors: GAO DAN , ZHAO ZHAN‐ZHENG , LIANG XIAN‐HUI , LI YAN , CAO YING , LIU ZHANG‐SUO
Published: July 2011

Aim:  The aim of this study is to investigate the expression of vascular endothelial growth factor (VEGF), basic fibroblast growth factor (bFGF) and endostatin (ES) in human peritoneum and investigate the relationship between them and peritoneum neoangiogensis in the patients with uraemia and peritoneal dialysis (PD).

Methods:  Peritoneal biopsies were obtained from normal subjects (n = 8), uraemic predialysis patients (n = 12) and PD patients (n = 10). The mRNA expression of VEGF, bFGF and ES in peritoneal tissues were measured through real‐time polymerase chain reaction. The protein expression of VEGF, bFGF and ES in peritoneal tissues were determined through western blot. Microvessel density (MVD) of peritoneal tissue was assessed using immunohistochemistry with CD34 monoclonal antibody.

Results:  The mRNA and protein of VEGF, bFGF and ES were expressed in all peritoneal samples. Compared with the normal control group, the mRNA and protein expression of VEGF and bFGF in peritoneal tissues were all significantly upregulated in the uraemic predialysis and PD group (all P < 0.05). Compared with the normal control group, the protein expression of ES were significantly upregulated in the uraemic predialysis and PD group (all (P < 0.05), but the mRNA expression of ES did not have obvious differences in the uraemic predialysis and PD group as compared to the normal control group (P > 0.05). MVD of peritoneal tissue were increased in the uraemic predialysis and PD group compared with the normal group (all P < 0.05). A significant positive correlation was found between VEGF mRNA expression and MVD, bFGF mRNA expression and MVD.

Conclusion:  The mRNA expression of VEGF and bFGF, the protein expression of VEGF, bFGF, and ES and microvessel density (MVD) are increased both in the uraemic predialysis and PD patients. These results show that uraemia circumstances and non‐physiological compatibility of peritoneal dialysis solution might increase VEGF, bFGF and ES expression and MVD, which might participate in the increment of the peritoneum neoangiogensis and ultrafiltration failure in PD patients.
Pollen source affects female reproductive success and early offspring traits in the rare endemic plantPolemonium vanbruntiae(Polemoniaceae)
Authors: BERMINGHAM LAURA HILL , BRODY ALISON K.
Published: July 2011

Understanding the relative magnitudes of inbreeding and outbreeding depression in rare plant populations is increasingly important for effective management strategies. There may be positive and negative effects of crossing individuals in fragmented populations. Conservation strategies may include introducing new genetic material into rare plant populations, which may be beneficial or detrimental based on whether hybrid offspring are of increased or decreased quality. Thus, it is important to determine the effects of pollen source on offspring fitness in rare plants. We established pollen crosses (i.e. geitonogamous‐self, autonomous‐self, intrasite‐outcross, intersite‐outcross and open‐pollinated controls) to determine the effects of pollen source on fitness (seeds/fruit and seed mass) and early offspring traits (probability of germination, number of leaves, leaf area and seedling height) in the rare plantPolemonium vanbruntiae. Open‐pollinated, intrasite‐outcross and geitonogamous‐self treatments did not differ in fitness. However, plants receiving autonomous‐self pollen had the lowest fitness and the lowest probability of seed germination. Intersite‐outcross plants contained fewer seeds/fruit, but seeds germinated at higher frequencies and seedlings were more vigorous. We also detected heterosis at the seed germination stage. These data may imply that natural populations ofP. vanbruntiaeexhibit low genetic variation and little gene flow. Evidence suggests that deleterious alleles were not responsible for reduced germination; rather environmental factors, dichogamy, herkogamy and/or lack of competition among pollen grains may have caused low germinability in selfed offspring. Although self‐pollination may provide some reproductive assurance inP. vanbruntiae, the result is a reduction in germination and size‐related early traits for selfed offspring.
Real‐time magnetic resonance imaging (MRI): anatomical changes during physiological voiding in men
Authors: Hocaoglu Yasemin , Roosen Alexander , Herrmann Karin , Tritschler Stefan , Stief Christian , Bauer Ricarda M.
Published: July 2011

Study Type – Diagnostic (exploratory cohort) Level of Evidence 2b

What’s known on the subject? and What does the study add?

Micturition cysturethrography or video urodynamics can show sequences of the micturition cycle, but are limited to show all participating structures at one. MRI is a non invasive imaging methodology to describe the anatomy of physiological voiding or voiding dysfunction.

In our study we provide preliminary insight in anatomical changes in the lower urinary tract during physiological micturition in males. This imaging methodology may help detecting anatomical differences in individuals with voiding disorders. Further, we presume that the vertical contraction of the ventral prostate seem to contribute to the initiation of successful micturition, additionally to the funnelling of the bladderneck.

OBJECTIVE

To investigate the interactions between the bladder, urethra, pelvic floor and the function of the prostate during ‘normal’ voiding.

PATIENTS AND METHODS

In all, 16 men with no history of urinary incontinence, urgency or obstructive voiding dysfunction were enrolled. We analysed the interaction between the bladder, urethra, pelvic floor and changes in the prostate during the Valsalva manoeuvre and voiding using real‐time magnetic resonance imaging (rtMRI).

The axis through the external sphincter (AES) to pubo‐coccygeal line (PC‐line) and the angle between the axis of the os pubis (AOP) and ventral prostate (VP) was measured before and at the end of voiding. Additionally, the angle between the AOP and the VP was measured during the Valsalva manoeuvre.

Change of position, or contraction, of the VP was measured.

RESULTS

The mean age of the men was 69.8 years and mean prostate volume 33.1 mL.

Before voiding, the mean AES to PC‐line was 10.5 mm. At the end of voiding, the mean AES to PC‐line was 20 mm.

The mean angle between AOP/VP was 31.6° in the storage phase and increased to a mean of 54.5° during voiding.

During the Valsalva manoeuvre, the angle between the AOP/VP remained constant.

There was a mean vertical contraction of the VP of 48.25 mm before voiding and a declining of the cranio‐caudal distance of the VP with a mean of 33.92 mm during voiding.

CONCLUSIONS

All the men in our study showed relaxation of the pelvic floor, followed by a descent of the bladder neck. Voiding could not be initiated unless the prostate rotated around the symphysis.

The study suggests that both the rotation and a vertical contraction of the prostate precede voiding.

The anatomy of physiological voiding or voiding dysfunction can be investigated non‐invasively using rtMRI.
Phosphodiesterase type 9 (PDE9) in the human lower urinary tract: an immunohistochemical study
Authors: Nagasaki Shuji , Nakano Youichi , Masuda Mariko , Ono Katsuhiko , Miki Yasuhiro , Shibahara Yukiko , Sasano Hironobu
Published: July 2011

What's known on the subject? and What does the study add?

Localization of PDE9 in human LUT has not been reported in the literature, although PDE5 was reported to be abundantly present only in smooth muscle cells using immunohistochemistry.

This is the first reported study which demonstrated the expression of PDE9 in the urothelium and neuron cells in the intramural ganglia of human LUT. Patterns of PDE9 localization were clearly different from those of PDE5, which suggest that functions of PDE9 were therefore considered to be different from those of PDE5 in human LUT.

OBJECTIVES

To examine the roles of the one of the cyclic guanosine monophosphate (cGMP)‐specific phosphodiesterases (PDEs), PDE9, in human lower urinary tract (LUT), we performed immunohistochemistry (IHC) using autopsy specimens.

To demonstrate the potential functional differences between PDE5 and PDE9 in human LUT, the localization of PDE5 and PDE9 was also compared using laser‐capture microdissection (LCM)/reverse transcriptase‐polymerase chain reaction (RT‐PCR) method.

MATERIALS AND METHODS

We immunolocalized PDE9 in human bladder (60 cases) and prostate (40) specimens using IHC.

We performed LCM/RT‐PCR evaluation in six human bladders to determine the differential expression patterns of PDE5 and PDE9.

RESULTS

PDE9 immunoreactivity was detected in the bladder urothelium of all the cases and in 85% of the prostatic urethral urothelium.

PDE9 immunoreactivity was detected in the perikaryon of the intramural ganglia.

LCM/RT‐PCR evaluation showed that PDE5 mRNA was exclusively detected in smooth muscle cells but PDE9 mRNA was mainly detected in the urothelium of the human bladder.

CONCLUSION

PDE9 is widely distributed in the urothelial epithelium of the human LUT and its potential roles may be different from those of PDE5.
Using asynchronous electronic surveys to help in‐class revision: A case study
Authors: Tong Vincent C. H.
Published: July 2011

Synchronous e‐voting systems (commonly known as ‘clickers’) have become increasingly popular as they can be used to enhance interactivity in lectures. Asynchronous electronic surveys (AESs), unlike these voting system, usually serve as a method of gathering feedback before or after teaching sessions. This paper describes and evaluates a project involving the use of AES with an integrated follow‐up lecture in an undergraduate science module. The study shows that the AES enhanced the students' learning experience by (1) prompting them to review previously taught material and (2) providing an engaging context for teaching in the follow‐up lecture. As AES can act as an effective link between module components, they can be used as a pedagogical device for improving the coherence of a curriculum. AES is, therefore, a valuable e‐learning platform, especially given the growing emphasis on interdisciplinary and multidisciplinary modules in recent years.

Practitioner Notes

What is already known about this topic

Electronic voting and surveys can either be conducted during the teaching (synchronous) or be employed before or after the teaching (asynchronous).

Synchronous voting devices, such as ‘clickers’, are widely used in lecturing.

Asynchronous electronic surveys (AESs) are mainly used in assessments and teaching evaluation.

What this paper adds

Novel implementation of AES: it can be used in conjunction with a follow‐up lecture.

Novel pedagogic application of AES: it can be used to help (1) students prepare for exams and (2) lecturers tailor their teaching to students' needs at the same time.

An evaluation of the students' perspectives on the use of AES with a follow‐up lecture in an undergraduate science module.

Implications for practice and/or policy

AES can be used to enhance the delivery of lectures as students may find the release of survey results an engaging experience.

It is a good practice to keep AES simple and anonymous.

AES with follow‐up lectures can provide effective links between different teaching components in a module.
The Monetary Analysis of Hyperinflation and the Appropriate Specification of the Demand for Money
Authors: Sokic Alexandre
Published: July 2011

This paper emerges from the failure of the traditional models of hyperinflation with perfect foresight. Insights from two standard optimizing monetary settings and economic reasoning from case studies of extreme hyperinflation episodes provide relevant requirements for the specification of the demand for money during hyperinflation. The paper demonstrates that the possibility of perfect foresight monetary hyperinflation paths depends robustly on the essentiality of money. The essentiality of money provides some depth of explanation of the reasons why the popular semi-log schedule of the demand for money is not appropriate for analysing monetary hyperinflation with perfect foresight. The paper proposes a simple test of money essentiality for the appropriate specification of the demand-for-money equation in empirical studies of hyperinflation.
Efficient Specialization in Ricardian Production
Authors: Richter Wolfram F. , Rosenmüller Joachim
Published: July 2011

It is well known that the analysis of efficient specialization in Ricardian production with many countries and many commodities cannot be broken down to the simple case of two countries and two commodities. By drawing on some recent results of convex geometry and the theory of cephoids, this paper characterizes efficient specialization in the general case.