bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatio-temporal expression analysis of two kinds of chemical communication-related proteins in the worker bee Apis cerana cerana Fabricius (Hymenoptera: Apidae)
Authors: Hong-Liang Li , Ya-Li Zhang , Hai-Yan Wang , Qi-Kang Gao , Jia-An Cheng 
Published: October 2009

AbstractThe spatio-temporal expressed profiles of two kinds of chemical communication-related protein genes, the odorant-binding protein of Ac-ASP2 and chemosensory protein of Ac-ASP3, were identified by real-time polymerase chain reaction (PCR). Results obtained using the 2−ΔΔCt method showed that Ac-ASP2 was a gene coding antenna-specific protein that did not express in larvae and pupae, but had discontinuous high abundance periods at 1, 9, 15, 27 and 30 days. The expressing abundance at such periods was at least ten times higher than that at other periods. From the distribution of Ac-ASP3 mRNA observed in different tissues, the transcript levels seemed to be higher in the wings, abdomen and thorax (of order ~106), and lower in the legs, antennae and head (of order ~105). From highest to lowest, the original copy number was found in the various body parts in the following order: wings, abdomen, thorax, legs, antenna, and head. The results suggest that Ac-ASP3 has an intimate relation with the chemosensory behaviour of wings and abdomen in Apis cerana cerana.
Cloning and tissue expression of the adiponectin gene in geese
Authors: Guo-Qing Xu , Dao-Qing Gong , Dong-Sheng Chu , Biao Dong , He Meng 
Published: October 2009

AbstractThree pairs of primers were designed for amplification of the adiponectin gene in geese (Anser demeatica) based on the published sequences of chicken, duck and other adiponectin homologues. The complete 1062 bp sequence of the adiponectin gene in geese, obtained by polymerase chain reaction (PCR) amplification and splicing, contained two exons and one intron. The coding sequence was 738 bp long and included codes for 245 amino acids (GenBank Accession No. EU370686). The coding sequence and the corresponding protein of goose adiponectin shared the highest homology with ducks, 94.85% and 95.51%, respectively; homology with chicken adiponectin was next highest, while the lowest homology was to be found with mammals. The predicted molecular weight (MW) and isoelectric point (pI) were 26,603.3 Da and pH 5.19, respectively, which were highly similar to those of species considered above. Reverse transcription-PCR revealed that goose adiponectin mRNA was highly expressed in skeletal muscle, fatty tissue, heart and stomach muscles. Medium levels of expression were detected in the small intestine, stomach glandular tissue, kidney and lung, while it was only weakly expressed in the liver, spleen, ovaries and diencephalon.
Cloning of carnation GA 20-oxidase and the construction of a plant RNAi vector
Authors: Liang Jin , Yun Liu , Zhen-Yuan Sun , Tian-Hong Li 
Published: October 2009

AbstractA pair of degenerate primers was designed based on a conserved domain of GA 20-oxidase reported in other plants. The full-length (1179 bp) carnation (Dianthus caryophyllus L. cv. Master) GA 20-oxidase cDNA (named Dc20ox) was cloned by reverse transcriptase-polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE). BLAST analysis revealed that the deduced amino acid sequence had high homology (66–75%) with the GA 20-oxidase sequences from other plants. An RNAi vector (pART400) was constructed from a 400 bp fragment representing a highly conserved region of GA 20-oxidase.
Identification and structure analysis of three tilapia species using microsatellite markers
Authors: Hong-Mei Song , Jun-Jie Bai , Ying-Chun Quan , Sheng-Jie Li 
Published: October 2009

AbstractSeventeen special loci were selected from 77 microsatellite markers to distinguish three varieties of tilapias, including the six differential loci UNH636, UNH117, UNH172, UNH738, UNH878 and UNH896 in Oreochromis aureus; five differential loci UNH913, UNH907, UNH222, UNH980 and UNH880 in O. niloticus; and six differential loci of UNH876, UNH899, UNH853, UNH932, UNH933 and UNH773 in O. mossambicus. Any one of the 17 loci could amplify particular bands to distinguish one tilapia from the other two. The genetic structure of O. aureus, O. niloticus and O. mossambicus stocks and their phylogenetic relationships were also analysed using these 17 loci. In total 142 alleles were detected, and the average number of alleles per locus was 8.35. Additionally, a clustering analysis was performed based on the result of the Popgen32 software package and phylogenetic trees were constructed by MEGA4 using the unweighted pair group method using arithmetic average (UPGMA). The results showed that the mean value of observed heterozygosity was 0.0941, 0.5490 and 0.2588, the mean value of expected heterozygosity was 0.1089, 0.7230 and 0.1965, and the polymorphism information content was 0.0869, 0.7149 and 0.1643, in O. aureus, O. niloticus and O. mossambicus, respectively. The UPGMA tree demonstrated that O. aureus was more closely related to O. mossambicus than to O. niloticus.
Influence of BCG dose and age of inoculated mice on immunoprotection against tuberculosis and expression of IFN-γ/IL-4
Authors: Hui-Jun Guo , Bao-Quan Li , Jia-Qian Chai , Wei-Shan Chang , Chun-Yang Wang , Hong-Mei Li 
Published: October 2009

AbstractBalB/C neonate mice and adult BalB/C mice were vaccinated using BCG (Bacille Calmette–Guerin). The pathogenic growth characteristics of BCG inin vitroculture on spleen cells (SPC) were observed and changes in induced expression of IFN (interferon)-γ and IL (interleukin)-4 in SPC were detected using the ELISPOT assay. The results showed that a low dose of BCG (2×103cfu) exerted 100% immunoprotection on 7-day-old neonate mice and a high dose of BCG (4×104cfu) exerted 75% immunoprotection. A low dose of BCG (2×103cfu) exerted 67% immunoprotection on 35-day-old mice. It is also shown that Th1-type cell immunity dominated by IFN-γ was enhanced significantly in the neonate mice injected with a low dose of BCG (2×103cfu), and Th2-type cell immunity dominated by IL-4 was depressed at the same time. IFN-γ and IL-4 induced by a high dosage of BCG (4×104cfu) in neonate mice were both increased. IFN-γ and IL-4 induced by a low dose of BCG (2×103cfu) in 35-day-old mice were also increased. The results indicate that there exists a marked correlation between immunoprotection by BCG in mice and both the immunizing dose and age of the immune animals, which might be relevant to the changes induced by BCG on Th1- and Th2-type cell immunity.
Annotation confidence score for genome annotation: a genome comparison approach
Authors: Yang Youngik , Gilbert Donald , Kim Sun 
Published: October 2009

Abstract
Motivation: The massively parallel sequencing technology can be used by small research labs to generate genome sequences of their research interest. However, annotation of genomes still relies on the manual process, which becomes a serious bottleneck to the high-throughput genome projects. Recently, automatic annotation methods are increasingly more accurate, but there are several issues. One important challenge in using automatic annotation methods is to distinguish annotation quality of ORFs or genes. The availability of such annotation quality of genes can reduce the human labor cost dramatically since manual inspection can focus only on genes with low-annotation quality scores.
Results: In this article, we propose a novel annotation quality or confidence scoring scheme, called Annotation Confidence Score (ACS), using a genome comparison approach. The scoring scheme is computed by combining sequence and textual annotation similarity using a modified version of a logistic curve. The most important feature of the proposed scoring scheme is to generate a score that reflects the excellence in annotation quality of genes by automatically adjusting the number of genomes used to compute the score and their phylogenetic distance. Extensive experiments with bacterial genomes showed that the proposed scoring scheme generated scores for annotation quality according to the quality of annotation regardless of the number of reference genomes and their phylogenetic distance.
Availability: http://microbial.informatics.indiana.edu/acs.
Contact: sumkim2@indiana.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Steady axisymmetric motion of a small bubble in a tube with flowing liquid
Authors: Feng James Q. 
Published: October 2009

The steady axisymmetric behaviour of a relatively small bubble moving with a flowing liquid in a straight round tube is studied by computationally solving the nonlinear Navier–Stokes equations, using a Galerkin finite-element method with boundary-fitted mesh, for wide ranges of capillary number
C
a
and Reynolds number
R
e
. Here a bubble is considered relatively small when its volume-equivalent radius is less than that of the tube. At small values of
R
e
, the velocity of a bubble increases with bubble size for large values of
C
a
but decreases with bubble size for small values of
C
a
. At large values of
R
e
, however, a bubble of large size appears to move at a slower velocity for any given value of
C
a
. When
R
e
is large (e.g.
R
e
= 100) and
C
a
> 0.1, a bubble of radius greater than half of the tube radius moves at a velocity that seems to be independent of bubble size. The strong inertial effect at large
R
e
makes a small bubble of radius greater than a quarter of the tube radius to deform into a noticeable oblate shape as
C
a
increases from very small value, and then to be elongated into a bullet shape with further increasing
C
a
after
C
a
reaches an intermediate value. Even very small bubbles (e.g. of radius equal to one-tenth of the tube radius) can still be significantly deformed provided that the value of
C
a
is adequately large. Despite significant shape deformations that may still occur, bubbles of radius less than a quarter of that of the tube almost always move at the same velocity as that of the local liquid flow at the tube centreline (i.e. twice that of the average liquid velocity), regardless the values of
R
e
and
C
a
. This fact suggests that very small bubbles are basically carried by the local liquid flow.
Three-dimensional Green's function and its derivative for materials with general anisotropic magneto-electro-elastic coupling
Authors: Buroni Federico C. , Sáez Andrés 
Published: October 2009

Explicit expressions of Green’s function and its derivative for three-dimensional infinite solids are presented in this paper. The medium is allowed to exhibit a fully magneto-electro-elastic (MEE) coupling and general anisotropic behaviour. In particular, new explicit expressions for the first-order derivative of Green’s function are proposed. The derivation combines extended Stroh formalism, Radon transform and Cauchy’s residue theory. In order to cover mathematical degenerate and non-degenerate materials in the Stroh formalism context, a multiple residue scheme is performed. Expressions are explicit in terms of Stroh’s eigenvalues, this being a feature of special interest in numerical applications such as boundary element methods. As a particular case, simplifications for MEE materials with transversely isotropic symmetry are derived. Details on the implementation and numerical stability of the proposed solutions for degenerate cases are studied.
Interleukin‐13: prospects for new treatments
Authors: Brightling C. E. , Saha S. , Hollins F. 
Published: October 2009

SummaryIL‐13 is a T‐helper type 2 cytokine. Animal models have implicated IL‐13 as a critical cytokine in the development of asthma and chronic obstructive pulmonary disease (COPD). In vitro IL‐13 exerts important effects on both structural and inflammatory cells within the airway and has the capacity to drive the clinical features of airways disease. In asthma, this view is strongly supported by associations with IL‐13 genetic polymorphisms and increased mRNA and protein expression in blood, sputum and bronchial submucosa. In particular, IL‐13 up‐regulation is associated with severe disease. Current evidence in COPD is conflicting, with some reports supporting and others refuting a role for IL‐13. Early clinical trials of anti‐IL‐13 therapies in asthma have shown promise, and the results of further efficacy studies are eagerly awaited. Cite this as: C. E. Brightling, S. Saha and F. Hollins, Clinical & Experimental Allergy, 2010 (40) 42–49.
Intravenous immunoglobulins – understanding properties and mechanisms
Authors: Durandy A , Kaveri S V , Kuijpers T W , Basta M , Miescher S , Ravetch J V , Rieben R 
Published: October 2009

SummaryHigh-dose intravenous immunoglobulin (IVIg) preparations are used currently for the treatment of autoimmune or inflammatory diseases. Despite numerous studies demonstrating efficacy, the precise mode of action of IVIg remains unclear. Paradoxically, IgG can exert both pro- and anti-inflammatory activities, depending on its concentration. The proinflammatory activity of low-dose IVIg requires complement activation or binding of the Fc fragment of IgG to IgG-specific receptors (FcγR) on innate immune effector cells. In contrast, when administered in high concentrations, IVIg has anti-inflammatory properties. How this anti-inflammatory effect is mediated has not yet been elucidated fully, and several mutually non-exclusive mechanisms have been proposed. This paper represents the proceedings of a session entitled ‘IVIg – Understanding properties and mechanisms’ at the 6th International Immunoglobulin Symposium that was held in Interlaken on 26–28 March 2009. The presentations addressed how IgG may affect the cellular compartment, evidence for IVIg-mediated scavenging of complement fragments, the role of the dimeric fraction of IVIg, the anti-inflammatory properties of the minor fraction of sialylated IgG molecules, and the genetic organization and variation in FcγRs. These findings demonstrate the considerable progress that has been made in understanding the mechanisms of action of IVIgs, and may influence future perspectives in the field of Ig therapy.
Conforming Falcon‡ gravity and the global gravity anomaly
Authors: Dransfield Mark 
Published: October 2009

ABSTRACTGravity derived only from airborne gravity gradient measurements with a normal error distribution will have an error that increases with wavelength. It is straightforward in principle to use sparsely sampled regional gravimeter data to provide the long wavelength information, thereby conforming the derived gravity to the regional gravity. Regional surface or airborne gravimeter data are not always available and can be difficult and expensive to collect in many of the areas where an airborne gravity gradiometer survey is flown. However the recent release by the Danish National Space Centre of the DNSC08 global gravity anomaly data has provided regional gravity data for the entire earth of adequate quality for this purpose. Studies over three areas, including comparisons with ground, marine and airborne gravimetry, demonstrate the validity of this approach. Future improvements in global gravity anomaly data are expected, particularly as the product from the recently launched Gravity field and steady‐state Ocean Circulation Explorer (GOCE) satellite becomes available and these will lead directly to an improvement in the very wide bandwidth gravity available after conforming gravity derived from gravity gradiometry with the global gravity.
Source measurement effect on high fidelity vibratory seismic separation
Authors: Nagarajappa Nirupama , Wilkinson David 
Published: October 2009

ABSTRACTHigh Fidelity Vibratory Seismic (HFVS) acquisition and separation can play an important role in today's land acquisition schemes. The method – in which multiple vibrators are swept simultaneously using sweeps with known phase encoding and then the data are inverted and separated into individual records – can improve productivity in the field and at the same time improve signal characteristics in the data. It relies on the measured weighted sum of accelerations (base plate and reaction mass) to invert the acquired data and separate the individual vibrator responses. Separation can be sub‐optimal if the measured motions vary from the ‘true source’ input into the ground. Differences in true source and measured source can arise due to poor coupling between vibrators and ground, soil compaction or other factors. Using both a synthetic model and real data, we show that if the true source changes between sweeps but is not measured, vibrator responses can leak into adjacent vibrator responses upon separation. In a recent survey with HFVS acquisition, we observed a 25–30 dB separation between adjacent vibrators, which could be improved with greater reliability of the source measurement. The vibrator leakage can reduce the data quality considerably. We discuss the results of this survey and show that separation is affected by source measurement error. Further, we conclude that it is necessary either 1) to use source measurements that can capture the variability of the true source between sweeps or 2) to compensate for the source measurement variations in processing or in acquisition.
Understanding Orobanche and Phelipanche–host plant interactions and developing resistance
Authors: PÉREZ‐DE‐LUQUE A , FONDEVILLA S , PÉREZ‐VICH B , ALY R , THOIRON S , SIMIER P , CASTILLEJO M A , FERNÁNDEZ‐Martinez J M , JORRÍN J , RUBIALES D , DELAVAULT P 
Published: October 2009

Summary Orobanche and Phelipanche spp. (broomrapes) are parasitic plants that can be responsible for devastating losses in several important crops. The development of resistant cultivars is one of the key strategies in the fight against this pest. However, the nature of resistance is complex and the basis of the interaction between the host and the parasite is still largely unknown. Despite the progress achieved during the last century through breeding programmes, sources of resistance are often scarce (e.g. the legumes). The resistance that is available is often not durable, with field resistance being overcome by new races of the parasite (e.g. sunflower). This review summarises efforts made to improve the resistance of crop hosts for broomrapes through classical breeding programmes and looks forward to the integration of new knowledge generated from molecular and morphological studies. Emphasis is given to the need for a multidisciplinary approach to achieve success, ranging from improved field phenotyping to genetic and biotechnological studies. All components are necessary to understand this particular and characteristic interaction: a plant parasitising another plant.
Extent and pattern of genetic differentiation within and between European populations of Phelipanche ramosa revealed by amplified fragment length polymorphism analysis
Authors: VAZ PATTO M C , FERNÁNDEZ‐APARICIO M , SATOVIC Z , RUBIALES D 
Published: October 2009

SummaryThe extent and pattern of genetic differentiation between Phelipanche ramosa populations colonising tobacco in different European regions were investigated by amplified fragment length polymorphism (AFLP) analysis, in order to determine levels of variation for tobacco resistance breeding and management programmes. Four different AFLP primer pairs amplified a total of 1050 clear and reproducible bands, of which 962 (91.62%) were polymorphic among the 35 individuals taken from four P. ramosa populations collected in Spain, Italy, Bulgaria and Germany. Cluster analysis based on the AFLP data categorised the plants into distinct groups, in line with their geographical origin, denoting clear genetic differentiation among the four populations. This differentiation was supported by both high bootstrap values and significant results of the analysis of molecular variance. The most divergent population was the one from Bulgaria. The majority of the genetic diversity was attributable to differences among populations (77.80%), as expected from the predominant autogamous behaviour of this species. Populations differed significantly in within‐population diversity, as measured by Shannon’s information index. The German population presented the lowest genetic diversity and the Italian population harboured the highest level of within‐population genetic diversity. There are significant differences in genetic diversity level among the studied P. ramosa populations and clear population‐specific genetic diversity structures. These need to be taken into account, together with the potential differences in parasite aggressiveness, when planning breeding and management strategies for P. ramosa control in tobacco cultivation.
Impact of Fusarium oxysporum on the holoparasitic weed Phelipanche ramosa: biocontrol efficacy under field‐grown conditions
Authors: KOHLSCHMID E , SAUERBORN J , MÜLLER‐STÖVER D 
Published: October 2009

SummaryUnder the changing agro‐climatic conditions of western Europe, the parasitic weed Phelipanche ramosa infests host crops such as tomato, hemp, tobacco and oilseed rape at an increasing rate. A Fusarium oxysporum isolate (FOG), that had effectively reduced the parasite’s incidence under controlled environmental conditions, was tested in different granular formulations (pesta granules, alginate pellets) on P. ramosa parasitising tobacco under field‐grown conditions. FOG reduced number and biomass of P. ramosa shoots by between 50% and 70% in three consecutive years (2006–2008). A single pesta application did not show consistent results throughout seasons; 50% reduction of P. ramosa biomass (DM) in the first year could not be repeated in the following years (20–30%). An alginate formulation applied alone performed better. However, a combination of pesta granules with alginate pellets had the highest reliable control efficacy (60–70%) of all treatments in two seasons, compared with the untreated control. Fungal population counts in soil samples did not show a close correlation to biocontrol efficacy. To understand field performance of this biocontrol agent, additional glasshouse and laboratory studies were conducted using soil from the experimental site. The glasshouse study revealed some fungistatic effects of the field soil that partly explain the reduced efficacy (‐40%) in the field compared with results obtained under controlled conditions. Results show the potential of FOG for P. ramosa control. Because formulation affected the biocontrol efficacy, it may be worthwhile to test how the delivery system can be changed in order to achieve increased disease development in the field.
Gene expression profiling of Medicago truncatula roots in response to the parasitic plant Orobanche crenata
Authors: DITA M A , DIE J V , ROMÁN B , KRAJINSKI F , KÜSTER H , MORENO M T , CUBERO J I , RUBIALES D 
Published: October 2009

Summary Orobanche crenata is a root parasitic weed that is a major constraint for grain and forage legume cultivation in Mediterranean and West Asia. Only moderate to low levels of incomplete resistance of complex inheritance has been identified so far in legume crops, which has hampered genetic and genomic analysis. In the present study, we provide a gene expression profile of roots of the model legume Medicago truncatula in response to infection by O. crenata. M. truncatula accessions SA27774 (complete resistance acting at early penetration stages) and SA4087 (incomplete late acting resistance mediated by necrosis of parasite tubercle) were inoculated with O. crenata seeds in a semi‐sterile dish system. Roots were harvested at 15 (first contacts of the parasitism structures with the host roots), 21 (initial stage of parasite tubercle formation on SA4087) and 35 (prior necrosis of well‐developed parasite tubercle of on SA4087) days post‐inoculation. Array hybridisations revealed several hundred genes up‐regulated in response to O. crenata infection. Gene expression patterns suggest that resistance mechanisms activated in both genotypes are temporally and spatially different and resemble those associated with plant resistance to microbial pathogens. Regulated genes identified here represent a comprehensive resource that can be used as a support to breeding strategies for resistance.