bluuebunny/crossref_metadata_2025 huggingface dataset:
Using trophic flows and ecosystem structure to model the effects of fishing in the Jurien Bay Marine Park, temperate Western Australia
Authors: Lozano-Montes Hector M. , Loneragan Neil R. , Babcock Russell C. , Jackson Kelsie
Published: May 2011

Understanding the impacts of fishing on the trophic structure of systems has become increasingly important because of the introduction of Ecosystem Based Fisheries Management and the legislative requirements of fisheries to demonstrate that they are not having a negative impact on other species. A biomass-based dynamic model of Jurien Bay Marine Park (∼30°S) was constructed using Ecopath to investigate the ecosystem impacts of fishing (mainly commercial rock lobster, Panulirus cygnus) in the park, as an example of the potential responses of temperate marine ecosystems in Western Australia to commercial fishing. A simulated 50% reduction in fishing mortality for commercial finfish predicted that after 20 years, the biomass of important fished species (i.e. Pagrus auratus and Choerodon rubescens) would increase by up to 30%. A simulated total fishing closure resulted in much larger (2.5–8 fold) increases in targeted populations, but did not result in any predicted cascading effects on grazing invertebrates and benthic primary producers. The simulations suggest that the structure of this ecosystem is characterised more by bottom-up than top-down processes; i.e. benthic primary production is a major limiting factor. The present study identified trophic linkages and ecosystem processes such as the role of both low and high trophic-level groups and the impact of fishing mortality in the marine park, an essential step towards distinguishing the impacts of fishing from those attributable to natural or other human-induced changes.
Predation as a driver of gastropod distribution in north-eastern New Zealand kelp forests
Authors: Freeman Debbie J. , Creese Robert G.
Published: May 2011

Gastropods play an important ecological role in kelp forests; however, this role is dependent on where exactly in such communities these animals are located. We assessed the spatial and temporal patterns in the utilisation of available reef and macroalgal substrates by three gastropods in a north-eastern New Zealand kelp (Ecklonia radiata (C. Agardh) J. Agardh, 1848) forest, focusing on predation as a factor influencing these patterns. Although kelp provided a large habitable surface area for gastropods, much of this area was under-utilised. During the day, gastropods on E. radiata were largely confined to the primary laminae. At night, gastropods on the reef migrated into the algal canopy where they occupied regions of the kelp that were not occupied during the day. Over a 36-day period, 93% of the gastropods tethered to the reef were consumed by predators, whereas none tethered in the algal canopy was consumed. We consider that night-time vertical migration and dispersion through the algal canopy may be primarily a response to predation by diurnally feeding fish and nocturnal benthic predators such as lobsters. Our research highlights the importance of considering diel changes in epifaunal distribution and abundance when assessing their ecological role.
A cost-effective alternative for assessing the size of deep-water fish aggregations
Authors: Hordyk Adrian R. , Loneragan Neil R. , Diver Geoff , Prince Jeremy D.
Published: May 2011

Acoustic methodologies are important tools for monitoring deep-water fish and have the potential to provide high-precision estimates of aggregation size. However, they can be costly to design and implement for monitoring fish. Data from 2 years of scientific surveys of the spawning aggregations of orange roughy (Hoplostethus atlanticus, Collett, 1889) on the Cascade Plateau, Tasmania, collected using commercial fishing vessels and echosounders, were used to develop a cost-effective approach for estimating the size of deep-water aggregations. Criteria were developed to standardise the identification of orange roughy echo-traces from acoustic data from 23 surveys in 2001 and 19 in 2005. The spawning condition of the fish was monitored simultaneously with the acoustics in each year (n = 29 trawls each year). The volumes of the aggregations were estimated throughout the survey period. Although the precision of the estimated aggregation size is low, large amounts of data can be collected over extended periods by using this approach and the equipment on standard commercial fishing echosounders. Aggregation volumes varied markedly during each spawning season and changes in volume appear to be linked to the spawning biology. Monitoring the spawning biology, therefore, provides crucial complementary information for interpreting estimates of aggregation size from acoustic surveys.
Calcium-dependent dynamics of cadherin interactions at cell–cell junctions
Authors: Kim Sally A. , Tai Chin-Yin , Mok Lee-Peng , Mosser Eric A. , Schuman Erin M.
Published: May 2011

Cadherins play a key role in the dynamics of cell–cell contact formation and remodeling of junctions and tissues. Cadherin–cadherin interactions are gated by extracellular Ca
2+
, which serves to rigidify the cadherin extracellular domains and promote
trans
junctional interactions. Here we describe the direct visualization and quantification of spatiotemporal dynamics of
N
-cadherin interactions across intercellular junctions in living cells using a genetically encodable FRET reporter system. Direct measurements of transjunctional cadherin interactions revealed a sudden, but partial, loss of homophilic interactions (τ = 1.17 ± 0.06 s
−1
) upon chelation of extracellular Ca
2+
. A cadherin mutant with reduced adhesive activity (W2A) exhibited a faster, more substantial loss of homophilic interactions (τ = 0.86 ± 0.02 s
−1
), suggesting two types of native cadherin interactions—one that is rapidly modulated by changes in extracellular Ca
2+
and another with relatively stable adhesive activity that is Ca
2+
independent. The Ca
2+
-sensitive dynamics of cadherin interactions were transmitted to the cell interior where β-catenin translocated to
N
-cadherin at the junction in both cells. These data indicate that cadherins can rapidly convey dynamic information about the extracellular environment to both cells that comprise a junction.
RETRACTED: Probing osmolyte participation in the unfolding transition state of a protein
Authors: Dougan Lorna , Genchev Georgi Z. , Lu Hui , Fernandez Julio M.
Published: May 2011

Understanding the molecular mechanisms of osmolyte protection in protein stability has proved to be challenging. In particular, little is known about the role of osmolytes in the structure of the unfolding transition state of a protein, the main determinant of its dynamics. We have developed an experimental protocol to directly probe the transition state of a protein in a range of osmolyte environments. We use an atomic force microscope in force-clamp mode to apply mechanical forces to the protein I27 and obtain force-dependent rate constants of protein unfolding. We measure the distance to the unfolding transition state, Δ
x

u

, along a 1D reaction coordinate imposed by mechanical force. We find that for the small osmolytes, ethylene glycol, propylene glycol, and glycerol, Δ
x

u

scales with the size of the molecule, whereas for larger osmolytes, sorbitol and sucrose, Δ
x

u

remains the same as that measured in water. These results are in agreement with steered molecular dynamics simulations that show that small osmolytes act as solvent bridges in the unfolding transition state structure, whereas only water molecules act as solvent bridges in large osmolyte environments. These results demonstrate that novel force protocols combined with solvent substitution can directly probe angstrom changes in unfolding transition state structure. This approach creates new opportunities to gain molecular level understanding of the action of osmolytes in biomolecular processes.
Intrinsic disorder in measles virus nucleocapsids
Authors: Jensen Malene Ringkjøbing , Communie Guillaume , Ribeiro Euripedes Almeida , Martinez Nicolas , Desfosses Ambroise , Salmon Loïc , Mollica Luca , Gabel Frank , Jamin Marc , Longhi Sonia , Ruigrok Rob W. H. , Blackledge Martin
Published: May 2011

The genome of measles virus is encapsidated by multiple copies of the nucleoprotein (N), forming helical nucleocapsids of molecular mass approaching 150 Megadalton. The intrinsically disordered C-terminal domain of N (N
TAIL
) is essential for transcription and replication of the virus via interaction with the phosphoprotein P of the viral polymerase complex. The molecular recognition element (MoRE) of N
TAIL
that binds P is situated 90 amino acids from the folded RNA-binding domain (N
CORE
) of N, raising questions about the functional role of this disordered chain. Here we report the first in situ structural characterization of N
TAIL
in the context of the entire N-RNA capsid. Using nuclear magnetic resonance spectroscopy, small angle scattering, and electron microscopy, we demonstrate that N
TAIL
is highly flexible in intact nucleocapsids and that the MoRE is in transient interaction with N
CORE
. We present a model in which the first 50 disordered amino acids of N
TAIL
are conformationally restricted as the chain escapes to the outside of the nucleocapsid via the interstitial space between successive N
CORE
helical turns. The model provides a structural framework for understanding the role of N
TAIL
in the initiation of viral transcription and replication, placing the flexible MoRE close to the viral RNA and, thus, positioning the polymerase complex in its functional environment.
Observations of multi-resonance effect in ELM control with magnetic perturbation fields on the JET tokamak
Authors: Liang Y. , Gimblett C.G. , Browning P.K. , Devoy P. , Alfier A. , Calabrò G. , Giroud C. , Harting D. , Koslowski H.R. , Jachmich S. , Pearson J. , Sun Y. , Wiegmann C. , Zhang T.
Published: May 2011

Multiple resonances of the edge-localized mode (ELM) frequency caused by the application of low n (=1 or 2) magnetic perturbations for ELM control have been observed on JET. With a low n field applied, a strong increase in ELM frequency, f
ELM, by a factor of ∼4.5 was found in many separated narrow windows of q
95 (resonant q
95), while the f
ELM increased only by a factor of ∼2 for non-resonant q
95 values. The fractions of increase in f
ELM with different resonant q
95 values are not the same. An analysis of ideal external peeling modes shows that both the dominant unstable peeling mode number and f
ELM depend on the amplitude of the normalized edge current density as well as the edge safety factor, q

a
.
Topology and transport in the edge region of RFX-mod helical regimes
Authors: Scarin P. , Vianello N. , Agostini M. , Spizzo G. , Spolaore M. , Zuin M. , Cappello S. , Carraro L. , Cavazzana R. , De Masi G. , Martines E. , Moresco M. , Munaretto S. , Puiatti M. E. , Valisa M.
Published: May 2011

New edge diagnostics and detailed analysis of magnetic topology have significantly improved the comprehension of the processes developing at the boundary of a reversed-field pinch (RFP) plasma in RFX-mod (a = 0.46 m, R = 2 m).

An upper critical density n
C ≈ 0.4 n
G (n
G Greenwald density) is found to limit the operational space for the improved quasi-single helical (QSH) regime: magnetic topology reconstructions and diagnostic observations suggest that this limit is due to a helical plasma–wall interaction which determines toroidally and poloidally localized edge density accumulation and cooling.

The experimental evidence is provided by a variety of diagnostics: the magnetic boundary as reconstructed from equilibrium codes reveals a helical deformation, which is well correlated with the modulation of edge pressure profile as reconstructed from the thermal helium beam diagnostic. Correlations with the helical deformation are also observed on the space- and time-resolved patterns of the floating potential measured at the wall, and with the edge plasma flow, obtained from different diagnostics. The relevance of these findings is that understanding the mechanisms that limit the operational space of QSH is decisive in achieving the goal of high-density stationary helical RFP equilibrium.
FTU results with a liquid lithium limiter
Authors: Mazzitelli G. , Apicella M.L. , Frigione D. , Maddaluno G. , Marinucci M. , Mazzotta C. , Pericoli Ridolfini V. , Romanelli M. , Szepesi G. , Tudisco O.
Published: May 2011

Since the end of 2005 most of the plasma–wall interaction experiments on FTU have been focused on the possible use of liquid lithium as the plasma facing material. Liquid lithium limiter is an active method to deposit, during the plasma discharge, a lithium film on the walls with prolonged beneficial effects. Reliable operation with very clean plasmas, very low wall particle recycling, spontaneous peaking of the density profile for line-averaged density values
have been obtained. These results have allowed us to extend the density limit to the highest value so far obtained (
at I
p = 0.7 MA and B
T = 7.1 T, q
a = 5.0, by gas puffing only) and to increase the energy confinement time by almost 50% with respect to the average value of 50 ms of the old ohmic FTU database. An accurate analysis of these plasmas has been carried out by means of a gyrokinetic code to establish the role of collisionality and density gradients on the observed phenomenology.
TheCaenorhabditis elegansGARP complex contains the conserved Vps51 subunit and is required to maintain lysosomal morphology
Authors: Luo L. , Hannemann M. , Koenig S. , Hegermann J. , Ailion M. , Cho M.-K. , Sasidharan N. , Zweckstetter M. , Rensing S. A. , Eimer S.
Published: May 2011

In yeast the Golgi-associated retrograde protein (GARP) complex is required for tethering of endosome-derived transport vesicles to the late Golgi. It consists of four subunits—Vps51p, Vps52p, Vps53p, and Vps54p—and shares similarities with other multimeric tethering complexes, such as the conserved oligomeric Golgi (COG) and the exocyst complex. Here we report the functional characterization of the GARP complex in the nematode Caenorhabditis elegans. Furthermore, we identified the C. elegans Vps51 subunit, which is conserved in all eukaryotes. GARP mutants are viable but show lysosomal defects. We show that GARP subunits bind specific sets of Golgi SNAREs within the yeast two-hybrid system. This suggests that the C. elegans GARP complex also facilitates tethering as well as SNARE complex assembly at the Golgi. The GARP and COG tethering complexes may have overlapping functions for retrograde endosome-to-Golgi retrieval, since loss of both complexes leads to a synthetic lethal phenotype.
Down-regulation of epithelial cadherin is required to initiate metastatic outgrowth of breast cancer
Authors: Wendt Michael K. , Taylor Molly A. , Schiemann Barbara J. , Schiemann William P.
Published: May 2011

Reduced epithelial cadherin (E-cad) is a hallmark of invasive carcinomas that have acquired epithelial-mesenchymal transition (EMT) phenotypes. Here we show that down-regulated E-cad expression induced by transforming growth factor-β (TGF-β) and EMT preceded breast cancer outgrowth in three-dimensional (3D) organotypic assays and in the lungs of mice. Pharmacological inhibitors against focal adhesion kinase prevented metastatic outgrowth of newly seeded organoids, but not that of their fully established counterparts. Interrogating the D2-HAN (hyperplastic alveolar nodule) model of breast cancer dormancy and metastasis showed that dormant D2.OR cells produced branched organoid morphologies in 3D-cultures, and expressed robust quantities of E-cad that was uncoupled from regulation by TGF-β. In contrast, metastatic D2.A1 organoids were spherical and wholly lacked E-cad expression. Interestingly, D2.A1 cells engineered to re-express E-cad formed branched organoids, down-regulated β1 integrin expression, and failed to undergo metastatic outgrowth. The tumor-suppressing function of E-cad was inactivated by increased microenvironmental rigidity, and was not recapitulated by expression of an E-cad mutant lacking its extracellular domain. Twist expression, but not that of Snail, reinitiated metastatic outgrowth in dormant D2.OR cells. Our findings show that EMT and its down-regulated expression of E-cad circumvent breast cancer dormancy in part by facilitating β1 integrin expression necessary for metastatic outgrowth.
Assessing Domestic Abuse in Women
Authors: Schroeder Knut
Published: May 2011

A44-year-old woman presents with an injury to her head. You also notice bruises around her neck and wrists. When you ask her about these, she bursts into tears, and you suspect possible domestic abuse.
Systematic Mutagenesis of All Predicted gntR Genes in Xanthomonas campestris pv. campestris Reveals a GntR Family Transcriptional Regulator Controlling Hypersensitive Response and Virulence
Authors: An Shi-Qi , Lu Guang-Tao , Su Hui-Zhao , Li Rui-Fang , He Yong-Qiang , Jiang Bo-Le , Tang Dong-Jie , Tang Ji-Liang
Published: May 2011

The GntR family is one of the most abundant and widely distributed groups of helix-turn-helix transcriptional regulators in bacteria. Six open reading frames in the genome of the plant pathogen Xanthomonas campestris pv. campestris were predicted to encode GntR regulators. All six of the predicted GntR-encoding genes were individually mutagenized and mutants from five of them were successfully obtained. Plant disease response assays revealed that one, whose product belongs to the YtrA subfamily and has been named HpaR1, is involved in the hypersensitive response (HR) and virulence. Electrophoretic mobility shift assays and in vitro transcription assays revealed that HpaR1 could repress its own transcription level through binding to its promoter sequence, indicating an autoregulatory feedback inhibition mechanism for HpaR1 expression. Promoter-gusA reporter and reverse-transcription polymerase chain reaction analyses revealed that HpaR1 positively and negatively affects the expression of HR and pathogenicity (hrp) genes in host plant and standard media, respectively. Constitutive expression of the key hrp regulator, hrpG, in the hpaR1 mutant could bypass the requirement of HpaR1 for the induction of wild-type HR, suggesting that HpaR1 regulates the expression of hrp genes that encode the type III secretion system via hrpG.
Specific and Sensitive Detection of Enterobacter mori Using Reliable RT-PCR
Authors: Lou M. M. , Jin G. L. , Tian W. X. , Zhang G. Q. , Fan X. Y. , Wang F. , Zhu B. , Xie G. L.
Published: May 2011

Enterobacter mori, the causal agent of bacterial wilt in mulberry, is becoming a serious disease in mulberry orchards in China. Because no effective control strategy has been devised for this disease, the reliable screening of mulberry material for latent infection became necessary. Hence, a fast polymerase chain reaction (PCR) assay for the detection of E. mori was developed in this study. The primers were designed within regions of the RNA polymerase β-subunit (rpoB) gene. The method is fast and simple and showed 100% sensitivity (no false negatives) and 100% specificity (no false positives), which was tested with 4 representative E. mori strains, 9 Enterobacter type strains, 2 strains of the other major mulberry bacterial pathogens (Ralstonia solanacearum and Pseudomonas syringae pv. mori) in China, 7 strains of other plant-associated pathogens, and 50 unidentified epiphytic bacterial isolates from mulberry plants. The real-time PCR assays reliably detected the DNA at at least 10 fg/μl and the bacterial cells at 102 CFU/ml from mulberry shoots and roots suspension. The strong positive reaction in testing of all symptomatic plants (with 100% positive) and parts of asymptomatic latent infected plant samples (with 36.4% positive) provided proof that this method is reliable and sensitive and suitable for screening plant material with latent infections of E. mori.
Whitefly Resistance Traits Derived from the Wild TomatoSolanum pimpinellifoliumAffect the Preference and Feeding Behavior ofBemisia tabaciand Reduce the Spread ofTomato yellow leaf curl virus
Authors: Rodríguez-López M. J. , Garzo E. , Bonani J. P. , Fereres A. , Fernández-Muñoz R. , Moriones E.
Published: May 2011

Breeding of tomato genotypes that limit whitefly (Bemisia tabaci) access and feeding might reduce the spread of Tomato yellow leaf curl virus (TYLCV), a begomovirus (genus Begomovirus, family Geminiviridae) that is the causal agent of tomato yellow leaf curl disease. TYLCV is restricted to the phloem and is transmitted in a persistent manner by B. tabaci. The tomato breeding line ABL 14-8 was developed by introgressing type IV leaf glandular trichomes and secretion of acylsucroses from the wild tomato Solanum pimpinellifolium accession TO-937 into the genetic background of the whitefly- and virus-susceptible tomato cultivar Moneymaker. Results of preference bioassays with ABL 14-8 versus Moneymaker indicated that presence of type IV glandular trichomes and the production of acylsucrose deterred the landing and settling of B. tabaci on ABL 14-8. Moreover, electrical penetration graph studies indicated that B. tabaci adults spent more time in nonprobing activities and showed a reduced ability to start probing. Such behavior resulted in a reduced ability to reach the phloem. The superficial type of resistance observed in ABL 14-8 against B. tabaci probing significantly reduced primary and secondary spread of TYLCV.
Validation and Clinical Utility of a Bowel Habit Questionnaire in School‐age Children
Authors: Wald Ellen R. , Jagodzinski Tanya D. , Moyer Stacey C.L. , Wald Arnold , Eickhoff Jens C. , Edmonson M. Bruce
Published: May 2011

Objectives:

The aim of the study was to validate a brief Bowel Habit Questionnaire (BHQ) with prospectively obtained data from a 14‐day diary and to determine whether the BHQ predicts the development of medically significant constipation (MSC) during the following year.

Materials and Methods:

The BHQ was distributed to parents of children ages 5 to 8 years during health supervision visits. Both the BHQ and subsequent diary were scored to indicate constipation if at least 2 of the following were reported: infrequent bowel movements, stool accidents, straining, avoidance, discomfort with defecation, or passing large stools >25% of the time. One year later, the BHQ was repeated to assess for MSC, defined as medical encounters about constipation or use of enemas, suppositories, laxatives, or stool softeners.

Results:

MSC was reported for 57 (13.7%) of 416 children on the first BHQ. Paired BHQ and diary data were obtained for 269 children; 54 (20.1%) had diary scores indicating constipation. BHQ had a sensitivity of 59.6% (95% confidence interval [CI] 46.7%–71.4%) and a specificity of 82.6% (95% CI 77.0%–87.1%). One year later, 11 children (5.2%) had developed new‐onset MSC; 7 (63.6%) of these children had initial BHQ scores of at least 2. Positive and negative predictive values for MSC were 19.4% (95% CI 9.8%–35.0%) and 97.7% (94.2%–99.1%), respectively.

Conclusions:

Parents often do not recognize constipation in young school‐age children and most constipated children remain untreated. A brief screening questionnaire in this population proved to be valid but only moderately sensitive; efforts to improve sensitivity are needed before recommending it for routine use.
Determination of a phosphorylation site in Nipah virus nucleoprotein and its involvement in virus transcription
Authors: Huang Mingshu , Sato Hiroki , Hagiwara Kyoji , Watanabe Akira , Sugai Akihiro , Ikeda Fusako , Kozuka-Hata Hiroko , Oyama Masaaki , Yoneda Misako , Kai Chieko
Published: May 2011

Many viruses use their host’s cellular machinery to regulate the functions of viral proteins. The phosphorylation of viral proteins is known to play a role in genome transcription and replication in paramyxoviruses. The paramyxovirus nucleoprotein (N), the most abundant protein in infected cells, is a component of the N–RNA complex and supports the transcription and replication of virus mRNA and genomic RNA. Recently, we reported that the phosphorylation of measles virus N is involved in the regulation of viral RNA synthesis. In this study, we report a rapid turnover of phosphorylation in the Nipah virus N (NiV-N). The phosphorylated NiV-N was hardly detectable in steady-state cells, but was detected after inhibition of cellular protein phosphatases. We identified a phosphorylated serine residue at Ser451 of NiV-N by peptide mass fingerprinting by electrospray ionization–quadrupole time-of-flight mass spectrometry. In the NiV minigenome assay, using luciferase as a reporter gene, the substitution of Ser451 for alanine in NiV-N resulted in a reduction in luciferase activity of approximately 45 % compared with the wild-type protein. Furthermore, the substitution of Ser451 for glutamic acid, which mimics a phosphoserine, led to a more significant decrease in luciferase activity – approximately 81 %. Northern blot analysis showed that both virus transcription and replication were reduced by these mutations. These results suggest that a rapid turnover of the phosphorylation of NiV-N plays an important role in virus transcription and replication.
A DNA methylation fingerprint of 1628 human samples
Authors: Fernandez Agustin F. , Assenov Yassen , Martin-Subero Jose Ignacio , Balint Balazs , Siebert Reiner , Taniguchi Hiroaki , Yamamoto Hiroyuki , Hidalgo Manuel , Tan Aik-Choon , Galm Oliver , Ferrer Isidre , Sanchez-Cespedes Montse , Villanueva Alberto , Carmona Javier , Sanchez-Mut Jose V. , Berdasco Maria , Moreno Victor , Capella Gabriel , Monk David , Ballestar Esteban , Ropero Santiago , Martinez Ramon , Sanchez-Carbayo Marta , Prosper Felipe , Agirre Xabier , Fraga Mario F. , Graña Osvaldo , Perez-Jurado Luis , Mora Jaume , Puig Susana , Prat Jaime , Badimon Lina , Puca Annibale A. , Meltzer Stephen J. , Lengauer Thomas , Bridgewater John , Bock Christoph , Esteller Manel
Published: May 2011

Most of the studies characterizing DNA methylation patterns have been restricted to particular genomic loci in a limited number of human samples and pathological conditions. Herein, we present a compromise between an extremely comprehensive study of a human sample population with an intermediate level of resolution of CpGs at the genomic level. We obtained a DNA methylation fingerprint of 1628 human samples in which we interrogated 1505 CpG sites. The DNA methylation patterns revealed show this epigenetic mark to be critical in tissue-type definition and stemness, particularly around transcription start sites that are not within a CpG island. For disease, the generated DNA methylation fingerprints show that, during tumorigenesis, human cancer cells underwent a progressive gain of promoter CpG-island hypermethylation and a loss of CpG methylation in non-CpG-island promoters. Although transformed cells are those in which DNA methylation disruption is more obvious, we observed that other common human diseases, such as neurological and autoimmune disorders, had their own distinct DNA methylation profiles. Most importantly, we provide proof of principle that the DNA methylation fingerprints obtained might be useful for translational purposes by showing that we are able to identify the tumor type origin of cancers of unknown primary origin (CUPs). Thus, the DNA methylation patterns identified across the largest spectrum of samples, tissues, and diseases reported to date constitute a baseline for developing higher-resolution DNA methylation maps and provide important clues concerning the contribution of CpG methylation to tissue identity and its changes in the most prevalent human diseases.
Magnetostratigraphy of the Neogene Chaka basin and its implications for mountain building processes in the north‐eastern Tibetan Plateau
Authors: Zhang Hui‐Ping , Craddock William H. , Lease Richard O. , Wang Wei‐tao , Yuan Dao‐Yang , Zhang Pei‐Zhen , Molnar Peter , Zheng De‐Wen , Zheng Wen‐Jun
Published: May 2011

Magnetostratigraphy of sedimentary rock deposited in the Chaka basin (north‐eastern Tibetan Plateau) indicates a late Miocene onset of basin formation and subsequent development of the adjacent Qinghai Nan Shan. Sedimentation in the basin initiated at ∼11 Ma. In the lower part of the basin fill, a coarsening‐upward sequence starting at ∼9 Ma, as well as rapid sedimentation rates, and northward paleocurrents, are consistent with continued growth of the Ela Shan to the south. In the upper section, several lines of evidence suggest that thrust faulting and topographic development of the Qinghai Nan Shan began at ∼6.1 Ma. Paleocurrent indicators, preserved in the basin in the proximal footwall of the Qinghai Nan Shan, show a change from northward to southward flow between 6.5 and 3.8 Ma. At the same location, sediment derived from the Qinghai Nan Shan appears at 6.1 Ma. Finally, the initiation of progressively shallowing dips observed in deformed basin strata and a change to pebbly, fluvial deposits at 6.1 Ma provide a minimum age for the onset of slip on the thrust fault that dips north‐east beneath the Qinghai Nan Shan. We interpret a decrease in sediment accumulation rates since ∼6 Ma to indicate a reduction in Chaka basin accommodation space due to active faulting and folding along the Qinghai Nan Shan and incorporation of the basin into the wedge‐top depozone. Declination anomalies indicate the beginning of counter‐clockwise rotation since 6.1 Ma, which we associate with local deformation, not regional block rotation. The emergence of the Qinghai Nan Shan near the end of the Miocene Epoch partitioned the once contiguous Chaka‐Gonghe and Qinghai basin complex. In a regional framework, our study adds to a growing body of evidence that points to widespread initiation and/or reactivation of fault networks during the late Miocene across the north‐eastern Tibetan Plateau.
Heparin‐induced thrombocytopenia: analysis of risk factors in medical inpatients
Authors: Kato Shumei , Takahashi Koichi , Ayabe Kengo , Samad Reza , Fukaya Eri , Friedmann Patricia , Varma Mala , Bergmann Steven R.
Published: May 2011

Heparin‐induced thrombocytopenia (HIT) is an unpredictable reaction to heparin characterized by thrombocytopenia and increased risk of life‐threatening venous and/or arterial thrombosis. Data are lacking regarding additional risk factors that may be associated with the development of HIT. This study aimed to identify the risk factors that may be associated with HIT in medical inpatients receiving heparin. Twenty five thousand six hundred and fifty‐three patients admitted to the medicine service who received heparin product were reviewed retrospectively. The diagnosis of HIT was confirmed if the platelet count dropped >50% from baseline and there was a positive laboratory HIT assay. Fifty‐five cases of in‐hospital HIT were observed. Multivariate analysis identified the administration of full anticoagulation dose with unfractionated heparin or exposure to heparin products for more than 5 d with an increased risk of HIT. Moreover, patients who were on haemodialysis, carried a diagnosis of autoimmune disease, gout or heart failure were also at increased risk. The results suggest that when using heparin products in these patient cohorts, increased surveillance for HIT is necessary.
Effects of inflammatory and anti‐inflammatory cytokines on the bone
Authors: Schett Georg
Published: May 2011

Eur J Clin Invest 2011; 41 (12): 1361–1366

Background  Inflammatory diseases are linked to enhanced bone loss. The effect of inflammation on bone is mediated by proinflammatory cytokines, which regulate bone formation as well as bone resorption thereby altering bone homeostasis.

Materials and methods  In this article we summarize the key insights in cytokine regulation of bone. We describe the major pro‐ and anti‐inflammatory mediators, which are involved in the regulation of bone and describe the mechanisms by which these cytokines alter bone balance.

Results  We describe the effects of tumor necrosis factor (TNF), interleukin (IL)‐ 1 family members, IL‐6, IL‐17 and interferons (IFN) on bone and discuss the mechanisms by which these individual cytokines affect the bone resorbing and the bone forming cells.

Conclusions  Several proinflammatory cytokines (such as TNFa, IL‐1 and IL‐17) are major triggers for osteoclast activation explaining the enhanced bone loss during inflammation. Other such as IL‐12, IL‐18, IL‐33 and IFN are strong suppressors of osteoclast differentiation and inhibit bone loss. Thus the cytokine composition of an inflammatory tissue is decisive whether inflammation triggers bone loss or not.
Insecticide‐treated vertical mesh barriers reduce the number of biting mosquitoes
Authors: FAIMAN R. , WARBURG A.
Published: May 2011

Mosquitoes foraging for blood sources normally fly relatively close to the ground where wind velocities do not exceed their flight speed. An experiment designed to block foraging mosquitoes from reaching inhabited houses was conducted in a rural settlement flanked by agricultural fields. Mosquitoes were collected during 9 nights using 30 carbon dioxide‐baited traps deployed along the external walls of six houses in the row closest to the settlement's perimeter fence. Thereafter, a deltamethrin‐impregnated mesh was draped along 400 m of the perimeter fence to a height of 2 m opposite three of the monitored houses. Mosquitoes were trapped for a further 11 nights. A significant difference in the numbers of mosquitoes caught before and after the intervention was demonstrated near protected houses, whereas no significant difference was observed in catches near control houses. The percentage of Culex perexiguus (Diptera: Culicidae), an important vector of West Nile virus, was significantly lower near protected houses (13%) than around control houses (45%). By contrast, the percentage of Culex pipiens was not significantly affected (16% at experimental and 18% at control houses). Although the results presented here are preliminary, the data demonstrate the potential efficacy of vertical insecticidal barriers for mosquito control.
Secular trends in age at menarche in women in the UK born 1908–93: results from the Breakthrough Generations Study
Authors: Morris Danielle H. , Jones Michael E. , Schoemaker Minouk J. , Ashworth Alan , Swerdlow Anthony J.
Published: May 2011

Morris DH, Jones ME, Schoemaker MJ, Ashworth A, Swerdlow AJ. Secular trends in age at menarche in women in the UK born 1908–93: results from the Breakthrough Generations Study. Paediatric and Perinatal Epidemiology 2011; 25: 394–400.

Menarcheal age decreased over time in Western countries until cohorts born in the mid‐20th century. It then stabilised, but limited data are available for recent cohorts. Menarche data were collected retrospectively by questionnaire in 2003–10 from 94 170 women who were participating in the Breakthrough Generations Study, aged 16–98 years, born 1908–93 and resident in the UK. Average menarcheal age declined from women born in 1908–19 (mean = 13.5 years) to those born in 1945–49 (mean = 12.6 years). It was then stable for several birth cohorts, but resumed its downward trend in recent cohorts (mean = 12.3 years in 1990–93 cohort). Trends differed between socio‐economic groups, but the recent decline was present in each group. In conclusion, menarcheal age appears to have decreased again in recent cohorts after a period of stabilisation.
In‐field distribution of Plasmodiophora brassicae measured using quantitative real‐time PCR
Authors: Wallenhammar A.‐C. , Almquist C. , Söderström M. , Jonsson A.
Published: May 2011

A protocol using real‐time polymerase chain reaction (PCR) for the direct detection and quantification of Plasmodiophora brassicae in soil samples was developed and used on naturally and artificially infested soil samples containing different concentrations of P. brassicae. Species‐specific primers and a TaqMan fluorogenic probe were designed to amplify a small region of P. brassicae ribosomal DNA. Total genomic DNA was extracted and purified from soil samples using commercial kits. The amount of pathogen DNA was quantified using a standard curve generated by including reactions containing different amounts of a plasmid carrying the P. brassicae target sequence. The PCR assay was optimized to give high amplification efficiency and three to four copies of the target DNA sequence were detected. Regression analysis showed that the standard curve was linear over at least six orders of magnitude (R2 > 0·99) and that the amplification efficiency was >92%. The detection limit in soil samples corresponded to 500 resting spores g−1 soil. The intersample reproducibility was similar to, or higher than, that of assays for other pathogens quantified in soil samples. Bait plants were used to validate the real‐time PCR assay. The protocol developed was used to investigate the spatial distribution of P. brassicae DNA in different fields and a significant difference was found between in‐field sampling points. The reproducibility of soil sampling was evaluated and showed no significant differences for samples with low levels of inoculum, whereas at higher levels differences occurred. Indicator kriging was used for mapping the probability of detecting P. brassicae within a 2‐ha area of a field. A threshold level of 5 fg plasmid DNA g−1 soil, corresponding to approximately 3 × 103P. brassicae resting spores g−1 soil, is suggested for growing resistant cultivars. The results provide a robust and reliable technique for predicting the risk of disease development and for assessing the distribution of disease within fields.
Net cadmium flux and accumulation reveal tissue‐specific oxidative stress and detoxification in Populus × canescens
Authors: He Jiali , Qin Jingjing , Long Lingyun , Ma Yonglu , Li Hong , Li Ke , Jiang Xiangning , Liu Tongxian , Polle Andrea , Liang Zongsuo , Luo Zhi‐Bin
Published: May 2011

To characterize the dynamics of Cd2+ flux in the rhizosphere and to study cadmium (Cd) plant‐internal partitioning in roots, wood, bark and leaves in relation to energy metabolism, reactive oxygen species (ROS) formation and antioxidants, Populus × canescens plantlets were exposed to either 0 or 50 µM CdSO4 for up to 20 days in the nutrient solution. A strong net Cd2+ influx in root apex was observed after Cd exposure for 24 h, even if net Cd2+ influx decreased gradually in roots. A large amount of Cd was accumulated in roots. Cd ions were uploaded via the xylem to leaves and further transported to the phloem where significant accumulation was detected. Cd accumulation led to decreased photosynthetic carbon assimilation but not to the depletion in soluble carbohydrates. Increased levels of ROS were present in all tissues, except the bark of Cd‐exposed poplars. To combat Cd‐induced superoxide and hydrogen peroxide, P.×canescens appeared to rely mainly on the formation of soluble phenolics as these compounds showed the highest accumulation in the bark and the lowest in wood. Other potential radical scavengers such as proline, sugar alcohols and antioxidant enzymes showed tissue‐ and exposure time‐specific responses to Cd. These results indicate a complex pattern of internal Cd allocation in P.×canescens resulting in higher ROS stress in wood than in bark and intermediate responses in roots and leaves, probably because of differential capacities of these tissues for the production of protective phenolic compounds.
Effective concentrations of garlic distillate (Allium sativum) for the control of Tetranychus urticae (Tetranychidae)
Authors: Attia S. , Grissa K. L. , Mailleux A. C. , Lognay G. , Heuskin S. , Mayoufi S. , Hance T.
Published: May 2011

The two‐spotted spider mite, Tetranychus urticae Koch, is a worldwide pest that feeds on a large variety of plant families. Because its resistance to acaricides is spreading rapidly, the development of new biological control tactics for population management is crucial. Plant extracts, such as garlic extract (Allium sativum Linn.), may represent viable alternatives, because they are currently considered to be minimum‐risk pesticides. Although garlic is known for its acaricidal properties, the extract concentration that provides the most efficient control has not yet been precisely determined.

In this study, we conducted a series of laboratory experiments to determine the susceptibility of adult females to different concentrations of garlic extract. Fresh garlic cloves were steam‐distilled and sprayed using a Potter spray tower. Mortality and fecundity were measured upon treatment with garlic extract concentrations ranging from 0.46 to 14.4 mg/l. Female mortality increased with concentration, with LD50 and LD90 values of 7.49 and 13.5 mg/l, respectively. Reduced fecundity was previously observed at concentrations of 0.36 and 0.74 mg/l.

The chemical composition of the Allium sativum distillate was characterized by reversed‐phase high‐performance liquid chromatography coupled with photodiode array detection, GC/MS and Fast GC‐FID against an authentic standard (Standard, Bioextract).Vinyl dithiin, diallyl disulphide, diallyl trisulphide and methyl allyl trisulphide were identified based on their mass spectra. Sesquiterpenoids were identified by their retention index.
Factors affecting the dispersal of large‐scale releases of the Queensland fruit fly, Bactrocera tryoni
Authors: Gilchrist A. S. , Meats A. W.
Published: May 2011

This study investigated two factors potentially affecting the spatial distribution of Queensland fruit fly Bactrocera tryoni (Froggatt) after release from a single point. First, the effect of age at release was investigated using a single cohort of 205 000 males from a mass‐rearing strain used for sterile insect releases. Approximately half were released as immature males and the remainder as sexually mature males (1 week later). Males were collected over 3 weeks from a grid of 135 traps, each containing a pheromone/insecticide bait, positioned between 4 and 500 m from the release point. Variation in the distribution of fly density around the release point was assessed by regressing trapped fly counts against distance. Unexpectedly, no significant differences were found in the spatial distribution of the flies. Second, the effect of inbreeding on spatial distribution was investigated using replicated simultaneous releases of two strains of B. tryoni. One strain was the existing (inbred) mass‐rearing strain that has been selected for high productivity in a mass‐rearing facility. The second strain was deliberately outbred but also selected for high productivity. Almost 100 000 males of each strain were released over the two experiments. Regression of trappings against distance differed significantly between strains in only one of five releases, but in all cases the outbred strain had a greater dispersal distance. As our trapping grid was not regular but contained gaps of up to 100 m, a small preliminary experiment investigated whether flies move faster along tree rows or across open fields. At distances up to 100 m, we found no detectable difference in fly distributions. These results are primarily relevant to the large‐scale point releases carried out as part of an existing B. tryoni sterile insect programme and are discussed in that context.
The Effect of Boar Seminal Plasma on the Release of Prostaglandins and Interleukin‐6 by Porcine Endometrial and Cervical Cells and Bovine Endometrial Cells
Authors: Madej M , Norrby M , Madsen MT , Johannisson A , Hansen C , Madej A
Published: May 2011

Contents

Artificial insemination (AI) of sows results in a significant elevation of prostaglandin F2α metabolite (PGFM) levels in peripheral plasma, whereas in mated sows such elevation is not seen. The aim of this study was to investigate whether boar seminal plasma (SP) has any effect on the release of PGFM, prostaglandin F2α (PGF2α), prostaglandin E2 (PGE2) or interleukin‐6 (IL‐6) by in vitro cultured porcine endometrial (epithelial – pUE and stromal – pUS), cervical (pCE and pCS) and bovine endometrial epithelial cells (bUE). This study shows that boar SP inhibits the release of PGFM, PGF2α and PGE2 by porcine endometrial and cervical cells and bovine endometrial cells after 3 and 24 h incubation. Boar SP stimulated IL‐6 release by pUE, pUS and even bUE after 3 h incubation. Tumour necrosis factor α (TNFα) stimulated the release of IL‐6 by pUS only after 24 h incubation, but in the presence of boar SP, this stimulation was attenuated. The overall results from these in vitro studies give us possibility to understand the difference in prostaglandin response between mated and inseminated sows. Furthermore, we demonstrated that frozen‐stored epithelial and stromal cells from pig endometrium, as well as from the cervix are suitable for studying the effect of SP on the release of prostaglandins. The only prerequisite is to incubate these thawed cells with arachidonic acid as a source for the synthesis of prostaglandins. A similar effect of boar SP on porcine and bUE cells may suggest inter‐species reactivity.
Fine‐Needle Aspiration Biopsy of Canine Mammary Gland Tumours: A Comparison Between Cytology and Histopathology
Authors: Sontas BH , Yüzbaşıoğlu Öztürk G , Toydemir TFS , Arun SS , Ekici H
Published: May 2011

Contents

In the current study, a total of 90 mammary neoplasms obtained from 55 female dogs were used to determine the accuracy of fine‐needle aspiration cytology in the diagnosis of canine mammary tumours and to investigate the feasibility of this technique for the differentiation of simple tumours from complex or mixed tumours. Three aspirations were performed on each mammary gland mass using a 22‐gauge needle attached to a 5‐ml syringe before the mammary glands were surgically excised and submitted for histopathological examination. Twenty‐five (27.7%) of 90 samples were classified as insufficient/inadequate for diagnosis. Of the remaining 65 samples, six (9.2%) were benign, 51 (78.5%) were malignant tumours and 8 (12.3%) were suspicious. Histopathological examination of the 90 specimens revealed five (5.6%) benign, 84 (93.3%) malignant and one (1.1%) non‐neoplastic lesion. The diagnostic accuracy, sensitivity and specificity of cytologic examination for diagnosing malignancy were 96.5%, 96.2% and 100%, respectively. However, when inadequate (n = 25) and suspicious (n = 8) samples were included, the diagnostic accuracy and sensitivity decreased to 63.3% and 60.7%, respectively, but no change was observed in the specificity. Furthermore, it was not possible to differentiate simple tumours from complex and mixed tumours because spindle cells were seen in both 28% of the simple tumours and 39.3% of the complex or mix tumours. In conclusion, we believe that fine‐needle aspiration cytology of canine mammary tumours is a valuable diagnostic tool, although our results indicated lower accuracy when inadequate samples were taken into consideration.
Characteristics and prognosis of patients with hepatocellular carcinoma after the year 2000 in Japan
Authors: Toyoda Hidenori , Kumada Takashi , Tada Toshifumi , Sone Yasuhiro , Kaneoka Yuji , Maeda Atsuyuki
Published: May 2011

Background and Aim:  The survival rate of patients with hepatocellular carcinoma (HCC) improved through the 1990s in Japan, primarily due to advances in the detection of small HCC under the establishment of surveillance systems. We investigated how the characteristics of patients with HCC changed and whether this trend is continuing after the year 2000.

Methods:  The characteristics and survival rates of patients with initial HCC (not a recurrence) who were diagnosed after the year 2000 until 2008 were analyzed and compared with those of patients in whom HCC was diagnosed in the 1990s or before.

Results:  In comparison to 8 years before the year 2000, the percentage of patients with better liver function at diagnosis of HCC increased after the year 2000, whereas the size of maximal HCC tumors did not change in comparison to patients before the year 2000. The survival rate of patients continued increasing after the year 2000.

Conclusions:  The prognosis of patients with HCC continues to improve after the year 2000. This is not due to further improvements in the detection of small‐sized HCC; the detection of small HCC had reached a plateau in the 1990s. Rather, this improvement appears to be due in part from the continued increase in the distribution of patients with better liver function at diagnosis.